10-Q

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

(MARK ONE)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2015

OR

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

FOR THE TRANSITION PERIOD FROM          TO          .

COMMISSION FILE NO. 0-28218

AFFYMETRIX, INC.

(Exact name of Registrant as specified in its charter)

DELAWARE	77-0319159
(State or other jurisdiction of	(I.R.S. Employer
incorporation or organization)	Identification Number)
3420 CENTRAL EXPRESSWAY
SANTA CLARA, CALIFORNIA 95051
(Address of principal executive offices and Zip Code)

Registrant’s telephone number, including area code: (408) 731-5000

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes x No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer o	Accelerated filer x
Non-accelerated filer o	Smaller reporting company o
(Do not check if a smaller reporting company)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No x

COMMON SHARES OUTSTANDING ON July 27, 2015: 79,820,002

AFFYMETRIX, INC.

TABLE OF CONTENTS

		Page No.
PART I. FINANCIAL INFORMATION		3
Item 1.	Financial Statements (unaudited)	3
	Condensed Consolidated Balance Sheets at June 30, 2015 and December 31, 2014	3
	Condensed Consolidated Statements of Operations for the Three and Six Months Ended June 30, 2015 and 2014	4
	Condensed Consolidated Statements of Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2015 and 2014	5
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2015 and 2014	6
	Notes to Condensed Consolidated Financial Statements	7
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	20
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	29
Item 4.	Controls and Procedures	29
PART II. OTHER INFORMATION		31
Item 1.	Legal Proceedings	31
Item1A.	Risk Factors	31
Item 2.	Mine Safety Disclosures	31
Item 3.	Other Information	31
Item 4.	Exhibits	31
SIGNATURES		31

PART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

AFFYMETRIX, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(In thousands)

	June 30, 2015			December 31, 2014
	(Unaudited)			(Note 1)
ASSETS:
Current assets:
Cash and cash equivalents	$	119,597		$	79,923
Accounts receivable, net	52,769			46,896
Inventories, net—short-term portion	54,030			50,676
Deferred tax assets—short-term portion	3,731			3,778
Prepaid expenses and other current assets	9,065			9,197
Total current assets	239,192			190,470
Property and equipment, net	20,861			18,087
Inventories, net—long-term portion	4,849			5,956
Goodwill	156,834			156,178
Intangible assets, net	107,920			106,183
Deferred tax assets—long-term portion	297			303
Other long-term assets	8,417			9,371
Total assets	$	538,370		$	486,548
LIABILITIES AND STOCKHOLDERS’ EQUITY:
Current liabilities:
Accounts payable and accrued liabilities	$	45,882		$	53,063
Current portion of long-term debt	4,000			4,000
Deferred revenue—short-term portion	8,128			9,210
Total current liabilities	58,010			66,273
Deferred revenue—long-term portion	2,348			2,372
Convertible notes	105,000			105,000
Term loan—long-term portion	16,950			18,950
Other long-term liabilities	20,601			21,626
Total liabilities	202,909			214,221
Stockholders’ equity:
Common stock	798			743
Additional paid-in capital	840,400			781,747
Accumulated other comprehensive loss	(7,578		)	(612		)
Accumulated deficit	(498,159		)	(509,551		)
Total stockholders’ equity	335,461			272,327
Total liabilities and stockholders’ equity	$	538,370		$	486,548

See accompanying Notes to the Condensed Consolidated Financial Statements

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AFFYMETRIX, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(In thousands, except per share amounts)

(Unaudited)

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015			2014
REVENUE:
Product sales	$	79,897	$	75,880		$	159,265		$	149,576
Services and other	9,069		9,552			18,419			18,827
Total revenue	88,966		85,432			177,684			168,403
COSTS AND EXPENSES:
Cost of product sales	27,156		30,560			54,741			60,071
Cost of services and other	4,731		6,028			11,027			12,932
Research and development	12,911		12,882			25,032			24,517
Selling, general and administrative	35,642		36,266			71,074			74,828
Litigation settlement	—		—			—			5,100
Total costs and expenses	80,440		85,736			161,874			177,448
Income (loss) from operations	8,526		(304		)	15,810			(9,045		)
Other income (expense), net	275		1,418			(398		)	1,711
Interest expense	1,471		1,623			2,953			3,377
Income (loss) before income taxes	7,330		(509		)	12,459			(10,711		)
Income tax provision	324		402			1,067			674
Net income (loss)	$	7,006	$	(911	)	$	11,392		$	(11,385	)
Basic net income (loss) per common share	$	0.09	$	(0.01	)	$	0.15		$	(0.16	)
Diluted net income (loss) per common share	$	0.08	$	(0.01	)	$	0.14		$	(0.16	)
Shares used in computing basic net income (loss) per common share	78,476		72,944			76,951			72,722
Shares used in computing diluted net income (loss) per common share	99,462		72,944			98,019			72,722

See accompanying Notes to the Condensed Consolidated Financial Statements

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AFFYMETRIX, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS)

(In thousands)

(Unaudited)

	Three Months Ended   June 30,						Six Months Ended   June 30,
	2015			2014			2015			2014
Net income (loss)	$	7,006		$	(911	)	$	11,392		$	(11,385	)
Other comprehensive income (loss), net of tax:
Foreign currency translation adjustment	1,510			(609		)	(6,612		)	(458		)
Unrealized change in available-for-sale and non-marketable securities (net of $0 tax for the three and six months ended June 30, 2015, respectively; net of tax of $(545) and $256 for the three and six months ended June 30, 2014, respectively)	37			(898		)	261			421
Unrealized change in cash flow hedges (net of $0 tax for the three and six months ended June 30, 2015 and 2014)	(2,403		)	181			(615		)	478
Net change in other comprehensive income (loss), net of tax	(856		)	(1,326		)	(6,966		)	441
Comprehensive income (loss)	$	6,150		$	(2,237	)	$	4,426		$	(10,944	)

See accompanying Notes to the Condensed Consolidated Financial Statements

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AFFYMETRIX, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

(Unaudited)

	Six Months Ended June 30,
	2015			2014
CASH FLOWS FROM OPERATING ACTIVITIES:
Net income (loss)	$	11,392		$	(11,385	)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization	10,855			16,521
Amortization of inventory step-up in fair value	—			4,666
Share-based compensation	7,287			6,272
Deferred tax, net	(818		)	(570		)
Gain on sales of securities	(54		)	(1,240		)
Other non-cash transactions	130			356
Changes in operating assets and liabilities:
Accounts receivable, net	(5,839		)	1,339
Inventories	(3,132		)	(1,207		)
Prepaid expenses and other assets	639			1,883
Accounts payable and accrued liabilities	(8,423		)	(2,599		)
Deferred revenue	(1,401		)	(6,136		)
Other long-term liabilities	500			(266		)
Net cash provided by operating activities	11,136			7,634
CASH FLOWS FROM INVESTING ACTIVITIES:
Acquisition of business	(14,000		)	—
Proceeds from sales of securities	—			2,162
Proceeds on sale of fixed assets	—			106
Capital expenditures	(6,092		)	(3,036		)
Purchase of technology rights	(341		)	—
Net cash used in investing activities	(20,433		)	(768		)
CASH FLOWS FROM FINANCING ACTIVITIES:
Issuance of common stock, net of issuance costs	51,421			1,978
Repayments of long-term debt	(2,000		)	(14,500		)
Net cash provided by (used in) financing activities	49,421			(12,522		)
Effect of exchange rate changes on cash and cash equivalents	(450		)	28
Net increase (decrease) in cash and cash equivalents	39,674			(5,628		)
Cash and cash equivalents at beginning of period	79,923			57,128
Cash and cash equivalents at end of period	$	119,597		$	51,500

See accompanying Notes to the Condensed Consolidated Financial Statements

6

AFFYMETRIX, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

JUNE 30, 2015

(UNAUDITED)

NOTE 1—SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles ("GAAP") for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited condensed consolidated financial statements include the accounts of Affymetrix, Inc. and its wholly-owned subsidiaries (“Affymetrix” or the “Company”). All significant intercompany accounts and transactions have been eliminated in consolidation. In the opinion of management, all adjustments, consisting of normal recurring entries, considered necessary for a fair presentation have been included.

Interim financial results are not necessarily indicative of results anticipated for the full year. These unaudited financial statements should be read in conjunction with the Company's audited financial statements and footnotes included in the Company's Annual Report on Form 10-K for the year ended December 31, 2014, from which the balance sheet information as of that date and as included herein was derived.

The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, and expenses, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.

There have been no material changes to the Company’s significant accounting policies as compared to the significant accounting policies described in the Company’s Annual Report on Form 10-K for the year ended December 31, 2014.

Comprehensive Income (Loss)

Comprehensive income (loss) is comprised of net income (loss) and other comprehensive income (loss) (“OCI”). OCI includes foreign currency translation adjustments, unrealized gains and losses on the Company's non-marketable securities and unrealized gains and losses on cash flow hedges that are excluded from net income (loss). Total comprehensive income (loss) has been disclosed in the Company's Condensed Consolidated Statements of Comprehensive Income (Loss).

The following table summarizes the amounts reclassified out of accumulated other comprehensive loss, net of tax, for the six months ended June 30, 2015 (in thousands):

	December 31, 2014			(Decrease)/ Increase			Reclassification Adjustments			June 30, 2015
Foreign currency translation adjustment	$	(2,933	)	$	(6,612	)	$	—		$	(9,545	)
Unrealized change in non-marketable securities	1,219			261			—			1,480
Unrealized change in cash flow hedges	1,102			2,054			(2,669		)	487
Total accumulated other comprehensive loss, net of tax	$	(612	)	$	(4,297	)	$	(2,669	)	$	(7,578	)

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2014-09, Revenue from Contracts with Customers (ASU 2014-09) to provide guidance on revenue recognition. ASU 2014-09 requires a company to recognize revenue when it transfers promised goods or services to customers in an amount that reflects

7

the consideration to which the company expects to be entitled in exchange for those goods or services. In doing so, companies will need to use more judgment and make more estimates than under today’s guidance. These may include identifying performance obligations in the contract, estimating the amount of variable consideration to include in the transaction price and allocating the transaction price to each separate performance obligation. In April 2015, the FASB proposed a one-year deferral of the effective date for ASU 2014-09. Under the proposal, ASU 2014-09 is effective for the Company in the first quarter of 2018. Early adoption up to the first quarter of 2017 is permitted. Upon adoption, ASU 2014-09 can be applied retrospectively to all periods presented or only to the most current period presented with the cumulative effect of changes reflected in the opening balance of retained earnings in the most current period presented. The Company is currently evaluating the method of adoption and the impact of adopting ASU 2014-09 on its consolidated financial statements.

In May 2015, the FASB issued Accounting Standards Update No. 2015-03, Interest - Imputation of Interest (ASU 2015-03) to provide guidance on the presentation of debt issuance costs. ASU 2015-03 requires a company to present debt issuance costs as a reduction from the carrying amount of the financial liability and not recorded as separate assets. ASU 2015-03 is effective for the Company in the first quarter of 2016. Early adoption is permitted. Upon adoption, ASU 2015-03 should be applied retrospectively to all periods presented. The Company's adoption of ASU 2015-03 would have resulted in a decrease in Other long-term assets, Convertible notes, and Term loan—long-term portion of $3.1 million as of June 30, 2015.

NOTE 2—ACQUISITION

On May 13, 2015 ("Acquisition Date"), the Company entered into an Asset Purchase Agreement with Eureka Genomics (“Eureka”), a developer of cost-effective, low- to mid-plex, high throughput genotyping assays that use next-generation sequencing (NGS) platforms for signal readout (the “Acquisition”). The Acquisition will extend the continuum of product offerings of the Company, enabling the Company to support more applications for current customers and also serve new customers.

The Acquisition was accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the tangible and intangible assets and liabilities of Eureka were recorded at their respective fair values as of the Acquisition Date, including an amount for goodwill representing the difference between the Acquisition consideration and the fair value of the net assets. The Company is in the process of determining the fair value of certain assets with the assistance of third-party specialists; thus, the June 30, 2015 reported fair values of acquired intangible assets and goodwill are provisional and subject to change.

The results of operations of the acquired Eureka business and the estimated fair values of the assets acquired and liabilities assumed have been included in the Company's condensed consolidated financial statements since the Acquisition Date. The results of operations for Eureka since the Acquisition Date are not material to the accompanying Condensed Consolidated Statement of Operations for the three and six months ended June 30, 2015.

Purchase Price

The total purchase price for Eureka was approximately $15.0 million of cash, including $14.0 million funded as of Acquisition Date through cash on hand and $1.0 million that has been held back, which is payable within 12 months of the Acquisition Date.

Fair values of assets acquired and liabilities assumed

Assets acquired and liabilities assumed were preliminarily recorded at their estimated fair values as of the Acquisition Date and include $11.2 million of identifiable intangible assets and $0.5 million of current liabilities with residual goodwill amounting to $4.3 million.

Identified intangible assets include in process research and development (“IPR&D) and customer relationships with preliminary estimated fair values of $10.4 million and $0.8 million respectively. These estimated fair values were determined using an income approach, which recognizes that the fair value of an asset is premised upon the expected receipt of future economic benefits such as earnings and cash inflows based on current sales projections and estimated direct costs. Indications of value are developed by discounting these benefits to their present worth at a discount rate that reflects the current return requirements of market participants. These assets are finite-lived intangible assets and are being amortized over their estimated useful lives ranging from ten to fifteen years.

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Goodwill

The excess of Acquisition consideration over the provisional fair value of assets acquired and liabilities assumed represents goodwill. The Company believes the factors that contributed to goodwill include synergies that are specific to the Company's consolidated business, and not available to other market participants, or other companies participating in the market, and the acquisition of a talented workforce that expands the Company's expertise in low- to mid-plex, high throughput genotyping assays. The Company expects this goodwill to be deductible for tax purposes in its entirety.

Transaction costs

The Company cumulatively incurred approximately $0.3 million of Acquisition-related costs that are reported in Selling, general and administrative expense in its Condensed Consolidated Statement of Operations, of which $0.2 million and $0.3 million was recognized in the three and six months ended June 30, 2015, respectively.

Pro Forma Financial Information (Unaudited)

The following unaudited pro forma financial information presents the combined results of operations for the three and six months ended June 30, 2015 and 2014 as if the Acquisition had been completed on January 1, 2014, with adjustments to give effect to pro forma events that are directly attributable to the Acquisition. The unaudited pro forma results do not reflect any operating efficiencies or potential cost savings that may result from the consolidation of the operations of the Company and Eureka. Accordingly, these unaudited pro forma results are presented for informational purposes only and are not necessarily indicative of what the actual results of operations of the combined company would have been if the Acquisition had occurred at the beginning of the period presented, nor are they indicative of future results of operations (in thousands, except per share data):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Revenues	$	89,064	$	85,464		$	178,069	$	168,454
Net income (loss)	6,335		(1,346		)	10,676		(12,570		)
Basic earnings per share	0.08		(0.02		)	0.14		(0.17		)
Diluted earnings per share	0.08		(0.02		)	0.13		(0.17		)

NOTE 3—FAIR VALUE MEASUREMENTS

Financial Assets and Liabilities Measured at Fair Value on a Recurring Basis

As of June 30, 2015 and December 31, 2014, assets and liabilities measured at fair value consisted of the following (in thousands):

	June 30, 2015						December 31, 2014
	Fair Value Measurements Using Input Types						Fair Value Measurements Using Input Types
	Level 2		Level 3		Total		Level 2		Level 3		Total
Assets:
Derivative assets	$	1,111	$	—	$	1,111	$	1,258	$	—	$	1,258
Non-marketable securities	—		3,698		3,698		—		3,384		3,384
Total assets	$	1,111	$	3,698	$	4,809	$	1,258	$	3,384	$	4,642
Liabilities:
Derivatives liabilities	$	433	$	—	$	433	$	—	$	—	$	—

9

Derivative financial instruments

The Company's derivative financial instruments are measured at fair value on a recurring basis utilizing Level 2 inputs as determined based on review of third-party sources. The fair value of the Company's derivative assets and liabilities is determined based on the estimated consideration the Company would pay or receive to terminate these agreements on the reporting date. The derivative assets and liabilities are located in Prepaid expenses and other current assets and Accounts payable and accrued expenses, respectively, in the accompanying Condensed Consolidated Balance Sheets.

Non-Marketable Securities

The Company believes the carrying amounts of its non-marketable securities approximated their fair values at the dates presented above. These non-marketable securities consist of an investment in a limited partnership investment fund that invests in companies in the life science industry and are located in the United States. The investments were initially valued at purchase price and subsequently on the basis of inputs that market participants would use in pricing such investments. The portfolio of investments includes Level 1 publicly-traded equity securities and Level 3 equity securities and notes.

During the year ended December 31, 2014, other-than-temporary impairment charges of $0.1 million were recognized on the Company's non-marketable securities. There were no other-than-temporary impairment charges during the six months ended June 30, 2015. Net investment losses are included in Other income (expense), net in the accompanying Consolidated Statements of Operations. Depending on market conditions, the Company may incur additional charges on this investment in the future.

The following table summarizes the change in the fair value of the Company's non-marketable securities during the six months ended June 30, 2015 (in thousands).

Balance as of December 31, 2014	$	3,384
Sales	—
Realized gains	54
Unrealized gains	260
Balance as of June 30, 2015	$	3,698

Fair Value of Long-Term Debt Obligations

As further discussed in Note 7, "Long-Term Debt Obligations", the Company's long-term debt obligations are not measured at fair value on a recurring basis and are carried at amortized cost. The Company believes the fair value of the Term Loan approximates its carrying value, or amortized cost, due to the short-term nature of these obligations and the market rates of interest they bear, and therefore is classified as Level 3 of the fair value hierarchy. The fair value of the Company’s 4.00% Notes is based on quoted market prices as of the respective balance sheet date, and therefore is classified as Level 1 of the fair value hierarchy. As of June 30, 2015, the fair value of the Company’s 4.00% Notes was approximately $209.9 million.

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NOTE 4—DERIVATIVE FINANCIAL INSTRUMENTS

The Company derives a portion of its revenues in foreign currencies, predominantly in Europe and Japan, as part of its ongoing business operations. In addition, a portion of its assets are held in the foreign currencies of its subsidiaries. The Company enters into foreign currency forward contracts to manage a portion of the volatility related to transactions that are denominated in foreign currencies. The Company’s foreign currency forward contracts are entered into for periods consistent with the related underlying exposures and do not constitute positions that are independent of those exposures.

The Company is exposed to the risk that the counterparties to its hedges may be unable to meet the terms of these agreements. To mitigate the risk, only contracts with carefully selected highly-rated major financial institutions are entered into. In the event of non-performance by these counterparties, the asset position carrying values of the financial instruments represent the maximum amount of loss that can be incurred; however, no losses as a result of counterparty defaults are expected. The Company does not require and is not required to pledge collateral for these financial instruments. The Company does not enter into foreign currency forward contracts for trading or speculative purposes and is not party to any leveraged derivative instruments.

As of June 30, 2015 and December 31, 2014, the total notional values of the Company’s derivative assets and liabilities were as follows (in thousands):

	June 30, 2015		December 31, 2014
Euro	$	28,636	$	15,982
Japanese Yen	4,960		3,391
British Pound	6,087		1,784
Total	$	39,683	$	21,157

The Company records all derivative assets and liabilities on the accompanying Condensed Consolidated Balance sheets at fair value. The following table shows the Company’s derivatives as of June 30, 2015 and December 31, 2014 (in thousands):

	June 30, 2015		December 31, 2014		Balance Sheet Classification
Derivative assets:
Foreign exchange contracts	$	1,111	$	1,258	Prepaid expenses and other current assets
Derivative liabilities:
Foreign exchange contracts	433		—		Accounts payable and accrued liabilities

The effective portions of designated cash flow hedges are recorded in OCI until the hedged item is recognized in operations. Derivatives that are not designated as hedging instruments and the ineffective portions of cash flow hedges are adjusted to fair value through operations.

Derivative instruments designated as cash flow hedges must be de-designated as hedges when it is probable the forecasted hedged transaction will not occur in the initially identified time period or within a subsequent two-month time period. Deferred gains and losses associated with such derivative instruments are reclassified immediately into operations through Other income (expense), net on the Condensed Consolidated Statements of Operations. Any subsequent changes in fair value of such derivative instruments are reflected in Other income (expense), net unless they are re-designated as hedges of other transactions.

All derivative assets and liabilities were designated as hedging relationships as of June 30, 2015 and December 31, 2014.

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The following table shows the effect, net of tax, of the Company’s derivative instruments on the accompanying Condensed Consolidated Statements of Operations and OCI for the three and sixmonths endedJune 30, 2015and 2014 (in thousands):

	Three Months Ended   June 30,						Six Months Ended   June 30,
	2015			2014			2015			2014
Derivatives in cash flow hedging relationships:
Net loss recognized in OCI	$	(2,403	)	$	(181	)	$	(615	)	$	(478	)
Net gain (loss) reclassified from accumulated OCI into Revenue	884			(314		)	2,669			(758		)
Net loss reclassified from accumulated OCI into Other income (expense), net	—			(7		)	—			(17		)
Net gain recognized in Other income (expense), net	49			19			62			1
Derivatives not designated as hedging relationships:
Net gain recognized in Other income (expense), net	—			11			—			12

As of June 30, 2015, the deferred amount recorded in OCI related to the Company's derivatives recorded is a net gain of $0.5 million and is expected to be recognized into earnings over the next 12 months.

NOTE 5—STOCKHOLDERS’ EQUITY AND SHARE-BASED COMPENSATION EXPENSE

At the Market Offering

On November 18, 2014, the Company entered into a sales agreement with Cantor Fitzgerald & Co. (“Cantor Fitzgerald”) to offer shares of its common stock, $0.01 par value per share, from time to time through Cantor Fitzgerald, as the Company’s sales agent for the offer and sale of the shares. The Company may offer and sell shares for an aggregate offering price of up to $50.0 million. The Company pays a commission equal to 3% of the gross proceeds from the sale of shares of its common stock under the sales agreement. The Company intends to use the net proceeds from this offering for general corporate purposes, including capital expenditures, debt repayments and working capital. The Company may also use a portion of the net proceeds from this offering to acquire or invest in complementary businesses, technologies, product candidates or other intellectual property, although there are no present commitments or agreements to do so. The Company is not obligated to make any sales of shares of common stock under the sales agreement. During the three months ended June 30, 2015, the Company sold a total of 1.6 million shares of common stock at an average price of $12.41 through its “at-the-market” offering, for total net proceeds of $19.4 million. During the first half of 2015, the Company sold a total of 3.8 million shares of common stock at an average price of $12.05 through its "at-the-market" offering, for total net proceeds of $44.7 million.

Share-based Compensation Plans

The Company has a share-based compensation program, most recently the 2000 Amended and Restated Equity Incentive Plan (the “Plan”), that provides the Board of Directors broad discretion in creating equity incentives for employees, officers, directors and consultants. This program includes incentive and non-qualified stock options and non-vested stock awards (also known as restricted stock) granted under various stock plans. As of June 30, 2015, the Company had approximately 6.6 million shares of common stock reserved for future issuance under its share-based compensation plans. New shares are issued as a result of stock option exercises, restricted stock units vesting and restricted stock award grants.

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The Company recognized share-based compensation expense in the accompanying Condensed Consolidated Statements of Operations for the three and six months ended June 30, 2015 and 2014, as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Costs of product sales	$	538	$	660	$	1,232	$	1,197
Research and development	408		637		923		1,144
Selling, general and administrative	2,278		1,830		5,132		3,931
Total share-based compensation expense	$	3,224	$	3,127	$	7,287	$	6,272

As of June 30, 2015, $17.5 million of total unrecognized share-based compensation expense related to non-vested awards is expected to be recognized over the respective vesting terms of each award through 2018. The weighted‑average terms of the unrecognized share-based compensation expense are 2.1 years for stock options and 1.9 years for restricted stock.

Performance-Based Awards

The Company's share-based awards program includes performance-based restricted stock awards ("PRSUs") that vest based upon the achievement of certain performance criteria and a service vesting criteria following the achievement of performance criteria. Performance criteria include various operational criteria of the Company such as revenues, earnings before interest, taxes, depreciation and amortization, earnings per share, and similar criteria, either on a Company-wide or business unit specific basis. The service vesting criteria ranges from two to four years. The Company recognizes the fair value of these awards to the extent the achievement of the related performance criteria is estimated to be probable. If a performance criteria is subsequently determined to not be probable of achievement, any related expense is reversed in the period such determination is made. Conversely, if a performance criteria is not currently expected to be achieved but is later determined to be probable of achievement, a “catch-up” entry is recorded in the period such determination is made for the expense that would have been recognized had the performance criteria been probable of achievement since the grant of the award.

2015 Program During the first quarter of 2015, the Compensation Committee granted certain PRSUs associated with performance criteria referred to as the 2015 Program. The purpose of the 2015 Program is to retain key employees. The measurement period for the 2015 Program is the twelve month period ending December 31, 2015 and the awards granted under the 2015 Program were granted in the form of performance shares pursuant to the terms of our 2000 Plan. Based on the achievement of the performance conditions, shares of stock would vest in equal installments over three years. The level of achievement of 2015 financial performance will be assessed during the first quarter of 2016 after which the shares of stock will be issued to the participants, contingent upon the recipient’s continued service to the Company. In 2015, the Company awarded 243,000 PRSUs under the 2015 Program at a grant date fair value of $11.88 per PRSU.

2015 CEO Grants During the second quarter of 2015, the Board of Directors approved a grant of PRSUs associated with performance criteria to the Company's Chief Executive Officer ("CEO") referred to as the 2015 CEO Grant. The measurement period for the 2015 CEO Grant is the twelve month period ending December 31, 2017 and the awards granted under the 2015 CEO Grant were granted in the form of performance shares pursuant to the terms of our 2000 Plan. The 2015 CEO Grant entitles the CEO to receive a certain number of shares of the Company's common stock based on the Company's satisfaction of certain financial performance goals as set and approved by the Board of Directors during the current quarter. Based on the achievement of the performance conditions during the Performance Period, the final settlement of the PRSU award will vest in February 2018. The level of achievement of 2017 financial performance will be assessed during the first quarter of 2018. The PRSU award will be forfeited if the performance goals are not met or if the CEO is no longer employed at the vest date. The Company awarded 156,023 PRSUs under the 2015 CEO Grant at a grant date fair value of $12.37 per PRSU.

As of June 30, 2015, there were 1,085,623 company-wide PRSUs outstanding with an average grant date fair value of $8.84 per PRSU. The Company expects that it is probable that 977,623 of these PRSUs will vest and that the related unrecognized stock compensation expense of $3.4 million will be recognized over the next three years. Changes in the Company’s assessment of the probability of achievement of performance criteria could have a material effect on the results of

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operations in future periods. There were no material changes in estimate related to the probability of vesting or recognition of expense related to PRSUs during either of the periods ended June 30, 2015 or 2014.

For additional information concerning the Company's share-based compensation plans, including performance-based awards programs, see Note 13, "Stockholders' Equity and Share-Based Compensation Expense", to the consolidated financial statements in Part II, Item 8 of the Company's 2014 Annual Report on Form 10-K.

NOTE 6—INVENTORIES

At June 30, 2015 and December 31, 2014, inventories, net consisted of the following (in thousands):

	June 30, 2015		December 31, 2014
Raw materials	$	11,299	$	11,461
Work-in-process	18,736		18,147
Finished goods	28,844		27,024
Total	$	58,879	$	56,632
Short-term portion	$	54,030	$	50,676
Long-term portion	$	4,849	$	5,956

During the six months ended June 30, 2014, amortization expense was approximately $4.7 million related to the fair value step-up of inventory acquired from eBioscience. The inventory fair value step-up was fully amortized as of June 30, 2014.

NOTE 7—WARRANTIES

The Company provides for anticipated warranty costs at the time the associated product revenue is recognized. Accrued warranties are included in Accounts payable and accrued liabilities in the accompanying Condensed Consolidated Balance Sheets. Product warranty costs are estimated based upon the Company’s historical experience and the applicable warranty period. The Company periodically reviews the adequacy of its warranty reserve and adjusts, if necessary, the warranty percentage and accrual based on actual experience and estimated costs to be incurred. Changes to the Company’s product warranty liability for the six months ended June 30, 2015 are as follows (in thousands):

Balance at December 31, 2014	$	912
Additions charged to cost of product sales	1,007
Repairs and replacements	(841		)
Balance at June 30, 2015	$	1,078

NOTE 8—LONG-TERM DEBT OBLIGATIONS

The following table summarizes the carrying amount of the Company's borrowings (in thousands):

	June 30, 2015		December 31, 2014
Term loan	$	20,950	$	22,950
Convertible notes	105,000		105,000
Total debt	125,950		127,950
Less: current portion of long-term debt	4,000		4,000
Total long-term debt	$	121,950	$	123,950

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Term Loan and Revolving Credit Facility

On June 25, 2012, in conjunction with the acquisition of eBioscience, Inc., the Company entered into a five year $100.0 million Senior Secured Credit Facility credit agreement (the “Credit Agreement”). The Credit Agreement provided for a Term Loan in an aggregate principal amount of $85.0 million and a revolving credit facility in an aggregate principal amount of $15.0 million.

On October 17, 2013, the Company refinanced its Senior Secured Credit Facility and entered into the Fourth Amendment to Credit Agreement (the "Fourth Amendment"). The Fourth Amendment provided, among other things, for a term loan in the aggregate principal amount of $38.0 million and revolving loan commitments in the aggregate principal amount of $10.0 million, each with a term of five years. The Company borrowed a total of $38.0 million under the Term Loan and $10.0 million under the revolving loan upon refinancing.

On July 28, 2014, the Company entered into the Fifth Amendment to Credit Agreement (the "Fifth Amendment" and the Credit Agreement as so amended, the "Amended Credit Agreement"). The Fifth Amendment provides, among other things, for (1) an uncommitted incremental term loan facility in an aggregate amount not to exceed $50.0 million and (2) the reduction of interest rate margins. As of June 30, 2015, the applicable interest rate was approximately 3.04%.

At the option of the Company (subject to certain limitations), borrowings under the Amended Credit Agreement bear interest at either a base rate or at the London Interbank Offered Rate (“LIBOR”), plus, in each case, an applicable margin. Under the Base Rate Option, interest will be at the base rate plus 1.5% to 1.75% dependent on the senior leverage ratio then in effect calculated on the basis of the actual number of days elapsed in a year of 365 or 366 days (as applicable) and payable quarterly in arrears. The base rate will be equal to the greatest of (a) the rate last quoted by The Wall Street Journal (or another national publication described in the Amended Credit Agreement) as the U.S. “Prime Rate,” (b) the federal funds rate, plus 0.50% per annum or (c) LIBOR for an interest period of one month, plus 1.00% per annum. Under the LIBOR Option, interest will be determined based on interest periods to be selected by Affymetrix of one, two, three or six months (and, to the extent available to all relevant lenders, nine or 12 years) and will be equal to LIBOR plus 2.50% and 2.75% dependent on the senior leverage ratio then in effect, calculated based on the actual number of days elapsed in a 360-day year. Interest will be paid at the end of each interest period or in the case of interest periods longer than three months, quarterly.

The loans and other obligations under the Senior Secured Credit Facility are (i) guaranteed by substantially all of the Company’s domestic subsidiaries (subject to certain exceptions and limitations) and (ii) secured by substantially all of the assets of Affymetrix and each guarantor (subject to certain exceptions and limitations).

The Amended Credit Agreement requires the Company to maintain an interest coverage ratio of at least 3.5 to 1.0 and a senior leverage ratio not exceeding initially 1.75 to 1.00 and stepping down to 1.20 to 1.00. The Amended Credit Agreement also includes other covenants, including negative covenants that, subject to certain exceptions, limit Affymetrix’, and that of certain of its subsidiaries’, ability to, among other things: (i) incur additional debt, including guarantees by the Company or its subsidiaries, (ii) make investments, pay dividends on capital stock, redeem or repurchase capital stock, redeem or repurchase the Company’s senior convertible notes or any subordinated obligations, (iii) create liens and negative pledges, (iv) make capital expenditures, (v) dispose of assets, (vi) make acquisitions, (vii) create or permit restrictions on the ability of Affymetrix’ subsidiaries to pay dividends or make distributions to Affymetrix, (viii) engage in transactions with affiliates, (ix) engage in sale and leaseback transactions, (x) consolidate or merge with or into other companies or sell all or substantially all the Company’s assets and (xi) change their nature of business, their organizational documents or their accounting policies.

The Company is required to make the following mandatory prepayments: (a) annual prepayments in an amount equal to 50% of excess cash flow (as defined in the Amended Credit Agreement), subject to leverage-based step-downs, (b) prepayments in an amount equal to 100% of the net cash proceeds of issuances or incurrences of debt obligations of Affymetrix and its subsidiaries (other than debt incurrences expressly permitted by the Credit Agreement), (c) prepayments in an amount equal to 100% of the net proceeds of asset sales in excess of $2.5 million annually (subject to certain reinvestment rights) and (d) prepayments in an amount equal to any indemnification payments or similar payments received under the Acquisition Agreement, subject to certain exclusions.

The Amended Credit Agreement also contains events of default, including payment defaults, breaches of representations and warranties, covenant defaults, cross-default and cross-acceleration to other indebtedness in excess of specified amounts, monetary judgment defaults in excess of specified amounts, bankruptcy or insolvency, actual or asserted

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invalidity or impairment of any part of the credit documentation (including the failure of any lien on a material portion of the collateral to remain perfected) and change of ownership or control defaults. In addition, the occurrence of a “fundamental change” under the indenture governing the 4.00% Convertible Notes would be an event of default under the Amended Credit Agreement. As of June 30 2015, the Company was in compliance with the covenants.

The proceeds received on June 25, 2012 from the original Term Loan were net of debt issuance costs of approximately $4.5 million being amortized over the 5-year term of the Senior Secured Credit Facility. Following the refinancing under the Fourth Amendment, the Company wrote off unamortized debt issuance costs of $2.5 million associated with the original Term Loan, and received proceeds on October 17, 2013 from the new Term Loan and Revolver, net of debt issuance costs of approximately $0.8 million that amortize on the effective interest rate method beginning October 17, 2013.

As of June 30, 2015, the Company had an outstanding principal balance of approximately $21.0 million under the Term Loan and incurred $0.3 million and $0.6 million in interest expense under the Senior Secured Credit Facility for the three and six months ended June 30, 2015, respectively. There were no amounts outstanding under the Revolving Credit Facility as of June 30, 2015.

Quarterly, principal payments are due under the Term Loan, which amortizes such that 10% of the outstanding principal is due during the first four years and the remaining 60% is due in the fifth year, including any remaining principal balance and any outstanding revolver balance at such time. The principal amount of unpaid maturities per the Amended Credit Agreement is as follows (in thousands):

2015, remainder thereof	$	—
2016	—
2017	—
2018	20,950
Total	$	20,950

The Company intends to continue making quarterly payments during 2015 and reclassified $4.0 million as current on the accompanying Condensed Consolidated Balance Sheet as of June 30, 2015.

4.00% Convertible Senior Notes

On June 25, 2012, the Company issued $105.0 million principal amount of 4.00% Convertible Senior Notes ("4.00% Convertible Notes") due July 1, 2019. The net proceeds, after debt issuance costs totaling $3.9 million from the 4.00% Convertible Notes offering, were $101.1 million. The 4.00% Convertible Notes bear interest of 4.00% per year payable semi-annually in arrears on January 1 and July 1 of each year, beginning on January 1, 2013 until the maturity date of July 1, 2019, unless converted, redeemed or repurchased earlier. The debt issuance costs are being amortized over the effective life of the 4.00% Convertible Notes, which is seven years.

Holders of the 4.00% Convertible Notes may convert their 4.00% Convertible Notes into shares of the Company’s stock at their option any time prior to the close of business on the business day immediately preceding the maturity date. The 4.00% Convertible Notes are initially convertible into approximately 170.0319 shares of the Company’s common stock per $1,000 principal amount of notes, which equates to 17,857,143 shares of common stock, or an initial conversion price of $5.88 per share of common stock. The conversion rate is subject to certain customary anti-dilution adjustments. In addition, following certain corporate events that occur prior to the maturity date, the Company will increase the conversion rate for a holder who elects to convert its notes in connection with such a corporate event in certain circumstances. Holders may also require the Company to repurchase for cash their notes upon certain fundamental changes.

On or after July 1, 2017, the Company can redeem for cash all or part of the 4.00% Convertible Notes if the last reported sale price per share of the Company’s common stock has been at least 130% of the conversion price then in effect for at least 20 trading days during any 30 consecutive trading day period ending within 5 trading days prior to the date on which the Company provides notice of redemption. The redemption price will be equal to 100% of the principal amount of the 4.00% Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. If the Company calls the 4.00% Notes for redemption, a holder of notes may convert its notes only until the close of business on the

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scheduled trading day immediately preceding the redemption date unless the Company fails to pay the redemption price (in which case a holder of notes may convert such notes until the redemption price has been paid or duly provided for).

As of June 30, 2015, the outstanding balance on the 4.00% Convertible Notes was $105.0 million and interest incurred for the three and six months ended June 30, 2015 was $1.2 million and $2.4 million, respectively.

NOTE 9—NET INCOME (LOSS) PER COMMON SHARE

Basic earnings per common share is calculated using the weighted‑average number of common shares outstanding during the period less the weighted‑average shares subject to repurchase. Diluted earnings per common share gives effect to dilutive common stock subject to repurchase, stock options (calculated based on the treasury stock method), shares purchased under the employee stock purchase plan and convertible debt (calculated using an as-if-converted method).

The following table sets forth a reconciliation of basic and diluted net income (loss) per common share (in thousands except per common share amounts):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Net income (loss)	$	7,006	$	(911	)	$	11,392	$	(11,385	)
Add effect of dilutive securities:
Interest on convertible notes	1,191		—			2,381		—
Adjusted net income (loss)	$	8,197	$	(911	)	$	13,773	$	(11,385	)
Shares used in computing basic net income (loss) per common share	78,476		72,944			76,951		72,722
Add effect of dilutive securities:
Employee stock options	1,559		—			1,604		—
Employee stock purchase plan	4					3		—
Restricted stock and restricted stock units	1,566		—			1,604		—
Convertible notes	17,857		—			17,857		—
Shares used in computing diluted net income (loss) per common share	99,462		72,944			98,019		72,722
Basic net income (loss) per common share	$	0.09	$	(0.01	)	$	0.15	$	(0.16	)
Diluted net income (loss) per common share	$	0.08	$	(0.01	)	$	0.14	$	(0.16	)

The potential dilutive securities excluded from diluted net income (loss) per common share were as follows (in thousands):

	Three Months Ended June 30,		Six Months Ended June 30,
	2015	2014	2015	2014
Employee stock options	1,841	4,540	1,796	4,540
Employee stock purchase plan	174	89	87	45
Restricted stock and restricted stock units	1,617	4,336	1,579	4,336
Convertible notes	—	17,857	—	17,857
Total	3,632	26,822	3,462	26,778

NOTE 10—LEGAL PROCEEDINGS

The Company has been in the past, and continues to be, a party to litigation, which has consumed, and may continue to consume, substantial financial and managerial resources. The Company could incur substantial costs and divert the attention of management and technical personnel in defending against litigation, and any adverse ruling or perception of an adverse ruling could have a material adverse impact on the Company’s stock price. In addition, any adverse ruling could have a material adverse impact on the Company’s cash flows and financial condition. The results of any litigation or any other

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legal proceedings are uncertain and, as of the date of this report, the Company has not accrued any liability with respect to any of the litigation matters listed below:

Enzo Litigation

Southern District of New York Case: On October 28, 2003, Enzo Life Sciences, Inc., a wholly-owned subsidiary of Enzo Biochem, Inc. (collectively "Enzo"), filed a complaint against the Company that is pending in the United States District Court for the Southern District of New York for breach of contract, injunctive relief and declaratory judgment. The Enzo complaint relates to a 1998 distributorship agreement with Enzo under which the Company served as a non-exclusive distributor of certain reagent labeling kits supplied by Enzo. On November 10, 2003, the Company filed a complaint against Enzo in the United States District Court for the Southern District of New York for declaratory judgment, breach of contract and injunctive relief relating to the 1998 agreement. On April 22, 2014, the Company entered into a settlement agreement with Enzo with respect to these two lawsuits. Pursuant to the agreement the Company agreed to pay Enzo $5.1 million and recorded the litigation settlement charge within the results of operations in the first three months of 2014. The settlement agreement does not include the Delaware Case described below.

Delaware Case: On April 6, 2012, Enzo filed a complaint against the Company in the United States District Court for the District of Delaware. In the complaint, plaintiff alleges that Affymetrix is infringing U.S. Patent No. 7,064,197 by making and selling certain GeneChip® products. The plaintiff seeks a preliminary and permanent injunction enjoining the Company from further infringement and unspecified monetary damages. The Company will vigorously defend against the plaintiff’s case. No trial date is set for this action.

Administrative Proceedings

The Company’s intellectual property is subject to a number of significant administrative actions. These proceedings could result in the Company’s patent protection being significantly modified or reduced, and the incurrence of significant costs and the consumption of substantial managerial resources. For the thee and six months ended June 30, 2015 and 2014, the Company did not incur significant costs in connection with administrative proceedings.

NOTE 11—INCOME TAXES

During the three and six months ended June 30, 2015, the Company recognized income tax expense of $0.3 million and $1.1 million, respectively. The provision for income taxes during the three and six months ended June 30, 2015 primarily consists of foreign taxes offset by a state income tax benefit upon audit closure of $0.5 million.

Due to the Company’s history of cumulative operating losses, management concluded that, after considering all the available objective evidence, it is not more likely than not that all the Company’s net deferred tax assets will be realized. Accordingly, all of the Company's U.S. deferred tax assets continue to be subject to a valuation allowance as of June 30, 2015.

As of June 30, 2015, the total amount of unrecognized tax benefits increased minimally compared to December 31, 2014. As a result of settlements of ongoing tax examinations and/or expiration of statues of limitations without the assessment of additional income taxes, the amount of unrecognized tax benefits that could be recognized in earnings in the next 12 months could range from zero to approximately $1.7 million.

NOTE 12—SEGMENT INFORMATION

The Company reports segment information on the "management" approach which designates the internal reporting used by management for making decisions and assessing performance as the source of the Company's reportable segments. The Company's chief operating decision maker ("CODM") is responsible for reviewing and approving investments in the Company's technology platforms and manufacturing infrastructure. The Company is organized into two reportable segments: Affymetrix Core and eBioscience.

Affymetrix Core is divided into four business units, with each business unit having its own strategic marketing and research and development groups to better serve customers and respond quickly to market needs. Affymetrix Core manufacturing operations are based on platforms that are used to produce various Affymetrix Core products that serve

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multiple applications and markets and similar customer and economic characteristics. Additionally, the business units share certain research, development, commercial operations and common corporate services that provide capital, infrastructure and functional support. As such, the Company concluded that the four business units represent one reportable operating segment. The following describes the four business units that form Affymetrix Core:

• Expression: This business unit markets the Company's GeneChip® gene expression products and services;

• Genetic Analysis and Clinical Applications: This business unit markets the Company's Axiom® genotyping product line, as well as products with clinical diagnostic and research applications including CytoScan® products, OncoScan® products, and the ViewRNA® in situ tissue hybridization platform for clinical translational research. In addition, the business unit is responsible for managing the Powered by Affymetrix™ (PbA) clinical partnering and licensing program which enables third-party diagnostic companies to access and develop DNA and RNA-based diagnostic tests based on Affymetrix technology platforms. This business unit also markets the CytoScan® Dx product, the recently FDA cleared microarray system as an aid for the post-natal diagnosis of children with developmental delays and intellectual disabilities;

• Life Science Reagents: This business unit sells reagents, enzymes, purification kits and biochemicals used by life science researchers and other biological and health care manufacturers, including those developing and marketing Next Generation Sequencing (“NGS”) products and molecular diagnostics; and

• Corporate: This business unit is comprised primarily of incidental revenue from royalty arrangements and field revenue from field-services provided to customers of the Company.

The eBioscience business unit operates with its own manufacturing, research and development, and marketing groups. The business unit does utilize certain Corporate functions such as finance, legal, commercial operations and human resources. This reportable segment specializes in the areas of flow cytometry reagents, immunoassays, microscopic imaging, other protein-based analyses, QuantiGene® single and multiplex RNA solution assays (not including the View RNA in situ tissue hybridization platform) and the ProcartaPlex™ multiplex immunoassay product lines.

All business units sell their products through the Global Commercial Organization comprised of sales, field application and engineering support personnel. The Company markets and distributes its products directly to customers in North America, Japan and major European markets. In these markets, the Company has its own sales, service and application support personnel responsible for expanding and managing their respective customer bases. In other markets, such as Mexico, India, Brazil, the Middle East and Asia Pacific, including China, the Company sells its products principally through third-party distributors that specialize in life science supply. The Company is selectively expanding its presence in the larger and more attractive markets, such as China. For certain molecular diagnostic and industrial opportunities, the Company supplies its partners with arrays and instruments, which they incorporate into diagnostic products or other routine applications and assume the primary commercialization responsibilities.

During 2015, the commercial organization and general and administrative functions are fully integrated. The Company no longer reports these operating expenses at a segment level and began evaluating the performance of its reportable segments based on revenue and gross profit. Revenue is allocated to each business unit based on product codes. The 2014 amounts have been recast to conform to the current presentation.

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The following table shows revenue and gross profit by reportable operating segment for the three and six months ended June 30, 2015 and 2014 (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Revenue:
Affymetrix Core	$	65,038	$	62,085	$	129,484	$	121,532
eBioscience	23,928		23,347		48,200		46,871
Total revenue	$	88,966	$	85,432	$	177,684	$	168,403
Gross Profit:
Affymetrix Core	$	42,507	$	37,230	$	83,133	$	72,234
eBioscience	14,572		11,614		28,783		23,166
Total gross profit	$	57,079	$	48,844	$	111,916	$	95,400

NOTE 13—RELATED PARTY TRANSACTIONS

In December 2011, the Company entered into an agreement under which it assigned one patent application and related know-how to Cellular Research, Inc. (“Cellular Research”), a company founded by the Company’s former Chairman, Dr. Stephen P.A. Fodor. Dr. Fodor also owns a majority of the shares of Cellular Research. Pursuant to the agreement, Cellular Research shall pay single digit royalties to Affymetrix on sales of products covered by the assigned technology, and starting in December 2016, an annual minimum fee of $100,000. Affymetrix shall also have a right of first refusal to collaborate with Cellular Research for the development of certain new products and to supply arrays to Cellular Research under certain terms and conditions. As of June 30, 2015, no significant royalties have been earned from this agreement.

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

This Management’s Discussion and Analysis of Financial Condition and Results of Operations as of June 30, 2015 and for the three and six months ended June 30, 2015 and 2014 should be read in conjunction with our financial statements and accompanying notes thereto included in this Quarterly Report on Form 10-Q and with the Management’s Discussion and Analysis of Financial Condition and Results of Operations included in our Annual Report on Form 10-K for the year ended December 31, 2014.

All statements in this quarterly report that are not historical in nature, are predicative in nature or that depend upon or refer to future events or conditions are "forward-looking statements" within the meaning of Section 21 of the Securities Exchange Act of 1934, as amended, and the Private Securities Litigation Reform Act of 1995. These include statements regarding our strategic initiatives, market expectations, integration of and synergies related to eBioscience, anticipated product and revenue growth, financial strength and regulatory environment, as well as all other "expectations," "beliefs," "hopes," "intentions," "strategies" and words of similar import and the negatives thereof. Such statements are based on our current expectations and are subject to a number of factors and uncertainties that could cause actual results to differ materially from those described in the forward-looking statements. We cannot assure you that actual results or business conditions will not differ materially from those projected or suggested in such forward-looking statements as a result of various factors, including, but not limited to, those discussed in “Risk Factors” contained in Part I, Item 1A of our Annual Report on Form 10-K for the year ended December 31, 2014. These forward-looking statements speak only as of the date of the Quarterly Report. Unless required by law, we do not undertake to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in our expectations with regard thereto or any change in events, conditions or circumstances on which any such statements are based.

OVERVIEW

We are a provider of life science and molecular diagnostic products that enable parallel analysis of biological systems at the gene, protein and cell level. We sell our products to life science research centers, academic institutions, government and private laboratories, as well as pharmaceutical, diagnostic and biotechnology companies. Over 94,500 peer-reviewed papers have been published based on work using our products. We have approximately 1,200 employees worldwide and maintain sales and distribution operations across the United States, Europe, Latin America and Asia.

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Acquisition of Eureka Genomics

On May 13, 2015, the Company entered into an Asset Purchase Agreement with Eureka, a developer of cost-effective, low- to mid-plex, high throughput genotyping assays that use common NGS platforms for signal readout. The Acquisition will extend the continuum of product offerings of the Company, enabling the Company to support more applications for current customers and also serve new customers.

The Acquisition was accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the tangible and intangible assets and liabilities of Eureka were recorded at their respective fair values as of the Acquisition Date, including an amount for goodwill representing the difference between the Acquisition consideration and the fair value of the net assets. The Company is in the process of determining the fair value of certain assets with the assistance of third-party specialists; thus, the June 30, 2015 reported fair values of acquired intangible assets and goodwill are provisional and subject to change.

The total purchase price for Eureka was approximately $15.0 million of cash, including $14.0 million funded as of Acquisition Date through cash on hand and $1.0 million that has been held back, which is payable within 12 months of the Acquisition Date. Assets acquired and liabilities assumed were preliminarily recorded at their estimated fair values as of the Acquisition Date and include $11.2 million of identifiable intangible assets and $0.5 million of current liabilities with residual goodwill amounting to $4.3 million.

Reportable Segments

See Note 11, "Segment Information", of the accompanying Condensed Consolidated Financial Statements for information on our reportable operating segments.

Our Strategy

Since Dr. Frank Whitney became our President and Chief Executive Officer in July 2011, our strategy has been to transform the company from one that is highly dependent on its GeneChip® Expression product line that faces intense competition in certain applications, to one with diversified revenue streams and a broad reach into the growing markets for translational medicine, molecular diagnostics, applied sciences, such as agricultural biotechnology ("AgBio") and single cell biology. For the twelve-month period ending December 31, 2011, our Expression business unit accounted for 46% of our business, while our Genetic Analysis and Clinical Applications business unit accounted for 27% of our business, and we did not have a presence in single cell biology. For the six-month period ending June 30, 2015, our Expression business unit accounted for 18% of our business, while our Genetic Analysis and Clinical Applications business unit accounted for 42% of our business, and eBioscience, with almost all its products focused on single cell biology, accounted for 27% of our business.

Since 2011, under the leadership of Dr. Witney, we have executed on a strategy to realign our product portfolio, stabilize our business and return our company to growth and profitability. We expect this transformation to take place over three phases, two of which are now completed:

• Phase 1 (2011-2012) –Portfolio Realignment. During this phase, we reorganized ourselves into business units to sharpen our focus based on target markets. We also launched CytoScan®HD, our cytogenetic microarray product line, enhanced our Axiom Genotyping Solution and acquired eBioscience. Through eBioscience, we offer flow cytometry reagents and immunoassay products which, aligned with our new product introductions, have enabled us to broaden our reach into the translational medicine market and address the large and growing single cell biology market. We believe these actions contributed to the stabilization of our business and the realignment of our product portfolio positioned us for growth.

• Phase II (2013-2014) – Profitability, Strengthen Balance Sheet, Development of Newer Product Lines. In the beginning of 2013, we implemented a corporate restructuring which resulted in significant cost savings and accelerated our path to profitability. In addition, we reduced our senior secured debt to $23.0 million as of December 31, 2014. We grew total revenue by 9% in 2014 compared to 2013, after adjustment for the divestiture of our Anatrace product line (which was sold in 2013) and a one-time license payment in 2013. This growth was driven by strong sales of CytoScan and Axiom Genotyping products and services, along with eBioscience products. We trained and refocused our internal research and development, marketing, operations and regulatory teams, along with our global commercial organization to expand our reach to customers in the translational medicine, molecular diagnostics and applied markets.

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• Phase III (2015 -2017) –Strategic Flexibility, Expansion of Product Lines, Growth. We entered Phase III of our transformation in 2015. In this phase, our goal is to leverage the work we have done in Phases I and II in order to have well established and growing franchises in: (1) translational medicine and molecular diagnostics (with a focus on reproductive health and oncology); (2) genotyping (both human and AgBio); and (3) single cell biology (the analysis of individual cells that comprise the population of cells typically studied by researchers, a market expected to grow rapidly over the next several years). We intend to continue the growth that we demonstrated in Phase II, as well as continue to improve our profitability. We strengthened our balance sheet in Phase II and are now in position to evaluate complimentary technology acquisitions that may enhance our positions in our target markets.

CRITICAL ACCOUNTING POLICIES AND ESTIMATES

Management's Discussion and Analysis of Financial Condition and Results of Operations is based upon our Condensed Consolidated Financial Statements, which we have prepared in accordance with U.S. generally accepted accounting principles ("GAAP"). The preparation of these financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

An accounting policy is deemed to be critical if it requires an accounting estimate to be made based on assumptions about matters that are highly uncertain at the time the estimate is made, if different estimates reasonably could have been used, or if changes in the estimate that are reasonably likely to occur could materially impact the financial statements. For a description of accounting changes and recent accounting standards, including the expected dates of adoption and estimated effects, if any, refer to Note 1, "Summary of Significant Accounting Policies", in the Notes to the Condensed Consolidated Financial Statements of this Quarterly Report on Form 10-Q. During the three and six months ended June 30, 2015, there have been no significant changes in our critical accounting policies and estimates compared to the disclosures in Item 7 of our Annual Report on Form 10-K for the year ended December 31, 2014.

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RESULTS OF OPERATIONS

The following discussion compares the historical results of operations for the three and six months ended June 30, 2015 and 2014.

REVENUE

	Three Months Ended June 30,				$ Change			% Change	Six Months Ended June 30,				$ Change			% Change
	2015		2014						2015		2014
Total revenue ($ in thousands):
Consumables	$	76,068	$	72,601	$	3,467		5%	$	152,523	$	142,488	$	10,035		7%
Instruments	3,829		3,279		550			17%	6,742		7,088		(346		)	(5)%
Product sales	79,897		75,880		4,017			5%	159,265		149,576		9,689			6%
Services and other revenue	9,069		9,552		(483		)	(5)%	18,419		18,827		(408		)	(2)%
Total revenue	$	88,966	$	85,432	$	3,534		4%	$	177,684	$	168,403	$	9,281		6%
Segment revenue ($ in thousands):
Affymetrix Core:
Expression	$	16,226	$	17,103	$	(877	)	(5)%	$	31,111	$	35,652	$	(4,541	)	(13)%
Genetic analysis and clinical applications	36,790		34,233		2,557			7%	73,745		64,454		9,291			14%
Life science reagents	7,109		6,851		258			4%	13,793		13,794		(1		)	0%
Corporate	4,913		3,898		1,015			26%	10,835		7,632		3,203			42%
Total Affymetrix Core	65,038		62,085		2,953			5%	129,484		121,532		7,952			7%
eBioscience	23,928		23,347		581			2%	48,200		46,871		1,329			3%
Total revenue	$	88,966	$	85,432	$	3,534		4%	$	177,684	$	168,403	$	9,281		6%
Segment revenue (% of revenue):
Affymetrix Core:
Expression	18%		20%						18%		21%
Genetic analysis and clinical applications	41%		40%						42%		38%
Life science reagents	8%		8%						8%		8%
Corporate	6%		5%						5%		5%
Total Affymetrix Core	73%		73%						73%		72%
eBioscience	27%		27%						27%		28%
Total revenue	100%		100%						100%		100%

Product sales

For the three months ended June 30, 2015, total product sales increased $4.0 million as compared to the same period in 2014. The increase was primarily due to a higher volume of sales of our PbA partners, Cytogenetics, ProcartaPlex and increased instruments revenue.

For the six months ended June 30, 2015, total product sales increased $9.7 million as compared to the same period in 2014. The increase was primarily due to a higher volume of sales of our Axiom Genotyping Solution products, our PbA partners, Cytogenetics and ProCartaPlex products. These increases were partially offset by a decline in our legacy IVT expression product sales and Gene and Exon arrays sales.

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Services and other revenue

For the three months ended June 30, 2015, services and other revenue decreased $0.5 million as compared to the same period in 2014, primarily due to decreased services revenue of $0.6 million, partially offset by higher royalty and license revenue of $0.1 million.

For the six months ended June 30, 2015, services and other revenue decreased $0.4 million as compared to the same period in 2014, primarily due to decreased field services revenue of $0.6 million, and professional services revenue of $0.2 million. This decrease was offset by higher royalty and license revenue of $0.4 million.

Expression

For the three months ended June 30, 2015, Expression revenue decreased $0.9 million as compared to the same period in 2014, primarily due to lower Gene and Exon arrays sales of $1.2 million and WT reagents sales of $0.3 million. This decrease was offset by higher IVT product sales of $0.6 million.

For the six months ended June 30, 2015, Expression revenue decreased $4.5 million as compared to the same period in 2014, primarily due to lower Gene and Exon arrays sales of $2.5 million, IVT sales of $1.1 million, instruments sales of $0.5 million, miRNA sales of $0.3 million and lower WT reagents sales of $0.4 million.

Genetic Analysis and Clinical Applications

For the three months ended June 30, 2015, Genetic Analysis and Clinical Applications revenue increased $2.6 million as compared to the same period in 2014, primarily due to increased PbA partners sales of $1.9 million, increased Cytogenetics product sales of $1.3 million, and increased instruments revenue of $1.0 million, partially offset by declines in sales of our legacy genotyping product SNP 6.0 of $0.6 million, Axiom® Genotyping Solution services sales of $0.7 million, and OncoScan sales of $0.7 million.

For the six months ended June 30, 2015, Genetic Analysis and Clinical Applications revenue increased $9.3 million as compared to the same period in 2014, primarily due to increased Axiom® Genotyping Solution product sales of $4.5 million, increased PbA partners sales of $4.0 million, increased Cytogenetics product sales of $2.6 million, and increased instruments revenue of $0.9 million, partially offset by declines in sales of our legacy genotyping product SNP 6.0 of $1.5 million, and OncoScan sales of $1.0 million.

Life Science Reagents

For the three months ended June 30, 2015, Life Science Reagents revenue increased $0.3 million as compared to the same period in 2014, primarily due to higher volume of molecular biology products.

For the six months ended June 30, 2015, Life Science Reagents revenue remained flat as compared to the same period in 2014, primarily due to higher volume of molecular biology products, offset by lower volume of biochemical products.

Corporate

For the three months ended June 30, 2015, Corporate revenue increased $1.0 million as compared to the same period in 2014, primarily due to a net realized gain from designated cash flow hedges of $1.2 million, partially offset by decreased field service revenue of $0.2 million.

For the six months ended June 30, 2015, Corporate revenue increased $3.2 million as compared to the same period in 2014, primarily due to a net realized gain from designated cash flow hedges of $3.4 million and increased royalty and license revenue of $0.4 million, partially offset by decreased field service revenue of $0.6 million.

eBioscience

For the three months ended June 30, 2015, eBioscience revenue increased $0.6 million as compared to the same period in 2014, primarily due to an increase in our ProCartaPlex sales of $0.4 million and QuantiGene ViewCell sales of $0.4 million.

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For the six months ended June 30, 2015, eBioscience revenue increased $1.3 million as compared to the same period in 2014, primarily due to an increase in our ProCartaPlex sales of $1.0 million, QuantiGene ViewCell sales of $0.8 million, and Flow Cytometry sales of $0.3 million, partially offset by a decrease in ELISA product sales of $1.0 million.

GROSS MARGIN

Management evaluates business segment performance based on revenue and gross margin. The following table presents gross margin for each reportable segment:

Dollars in thousands	Three Months Ended June 30,						$ % Change		Six Months Ended June 30,						$ % Change
	2015			2014					2015			2014
Total gross profit:
Product	$	52,741		$	45,320		$	7,421	$	104,524		$	89,505		$	15,019
Services and other	4,338			3,524			814		7,392			5,895			1,497
Total gross profit	$	57,079		$	48,844		$	8,235	$	111,916		$	95,400		$	16,516
Product gross margin	66		%	60		%	6		66		%	60		%	6
Service and other gross margin	48		%	37		%	11		40		%	31		%	9
Segment gross profit:
Affymetrix Core	$	42,507		$	37,230		$	5,277	$	83,133		$	72,234		$	10,899
eBioscience	14,572			11,614			$	2,958	28,783			23,166			5,617
Total gross profit	$	57,079		$	48,844		$	8,235	$	111,916		$	95,400		$	16,516
Affymetrix Core gross margin	65		%	60		%	5		64		%	59		%	5
eBioscience gross margin	61		%	50		%	11		60		%	49		%	11

Product gross profit

For the three months ended June 30, 2015, product gross profit increased $7.4 million as compared to the same period in 2014, consisting of $4.7 million increase due to higher sales and improved product mix and $1.8 million increase due to the completion of amortization for the step-up in inventory fair value that was recognized when we acquired eBioscience in 2012. In addition, manufacturing variances were favorable by $1.5 million due to productivity improvements and larger batch sizes for our Reagents manufacturing.

For the six months ended June 30, 2015, product gross profit increased $15.0 million as compared to the same period in 2014, consisting of $11.5 million increase due to higher sales and product mix and $4.7 million due to the completion of amortization for the step-up in inventory fair value that was recognized when we acquired eBioscience in 2012. The increases were partially offset by a decrease due to higher warranty expense of $1.1 million for arrays and instruments.

Service and other gross profit

For the three months ended June 30, 2015, service gross profit increased $0.8 million as compared to the same period in 2014, primarily due to lower expenses on supplies and reduction in temporary labor due to the completion of a large biobank project of $1.3 million. These increases were partially offset by reduced field services gross profit of $0.3 million due to unfavorable foreign exchange and lower professional services gross profit of $0.3 million.

For the six months ended June 30, 2015, service gross profit increased $1.5 million as compared to the same period in 2014, primarily due to lower expenses on supplies and reduction in temporary labor for the service lab related to the completion of a large biobank project of $2.0 million, and increased royalties revenue of $0.4 million. These increases were partially offset by reduced field services gross profit of $0.6 million and lower professional service gross profit of $0.3 million.

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Affymetrix Core

For the three months ended June 30, 2015, Affymetrix Core gross profit increased $5.3 million as compared to the same period in 2014, consisting of $3.5 million due to increased sales and improved product mix, $1.3 million due to lower spending on supplies and reduction in temporary labor related to the completion of a large biobank project, $1.2 million from favorable manufacturing variances due to improved productivity and larger batch sizes for Reagents manufacturing, $0.7 million from favorable standard cost amortization due to a write down in the second quarter of 2014. These increases were partially offset by a decrease of $1.1 million due to higher warranty activities in the current period and a decrease of $0.7 million primarily due to inventory write-offs.

For the six months ended June 30, 2015, Affymetrix Core gross profit increased $10.9 million as compared to the same period in 2014, consisting of $9.2 million due to increased sales, improved product mix, and lower costs driven by higher utilization of our Singapore and Ohio factories as well as lower costs due to full amortization of certain license payment in the prior years which was not recurring in the current period, $2.0 million due to lower spending on supplies and reduction in temporary labor related to the completion of a large biobank project, $1.5 million from favorable standard cost amortization due to a write down in the prior year. These increases were partially offset by a decrease of $1.1 million due to higher warranty activities in the current period and a decrease of $0.6 million primarily due to inventory write-offs.

eBioscience

For the three months ended June 30, 2015, eBioscience gross profit increased $3.0 million as compared to the same period in 2014, consisting of $1.8 million increase due to the completion of amortization for the step-up in inventory fair value that was recognized when we acquired eBioscience in 2012, $1.2 million increase due to higher sales, and $0.8 million increase due to lower excess and obsolescence reserve in the current period. These increases were partially offset by a decrease due to the change in standard cost amortization of $0.7 million.

For the six months ended June 30, 2015, eBioscience gross profit increased $5.6 million as compared to the same period in 2014, consisting of $4.7 million increase due to the completion of amortization for the step-up in inventory fair value that was recognized when we acquired eBioscience in 2012, $1.7 million increase due to higher sales, and $0.9 million increase due to lower excess and obsolescence reserve in the current period. These increases were partially offset by a decrease of $1.4 million due to the change in standard cost amortization and a decrease of $0.6 million due to unfavorable factory absorption.

OPERATING EXPENSES

Dollars in thousands	Three Months Ended June 30,				$ Change			% Change	Six Months Ended June 30,				$ Change			% Change
	2015		2014						2015		2014
Research and development	$	12,911	$	12,882	$	29		0%	$	25,032	$	24,517	$	515		2%
Selling, general and administrative expenses	35,642		36,266		(624		)	(2)%	71,074		74,828		(3,754		)	(5)%
Litigation settlement	—		—		—			0%	—		5,100		(5,100		)	100%

Research and development Research and development expense remained flat for the three months ended June 30, 2015 as compared to the same period in 2014. This is primarily due to higher compensation and benefits related to additional headcount assumed post the Acquisition of Eureka Genomics and higher spending on supplies, offset by decreased consulting and external services. Research and development expense increased $0.5 million for the six months ended June 30, 2015 as compared to the same period in 2014. The increase is primarily due to higher spending on supplies and increased consulting and external services.

Selling, general and administrative Selling, general and administrative expenses decreased $0.6 million for the three months ended June 30, 2015 as compared to the same period in 2014. The decrease is primarily due to lower legal fees incurred during the current period and lower depreciation expense as certain fixed assets have been fully depreciated, partially offset by increases in compensation and benefits related to additional headcount assumed post Acquisition. Selling, general and administrative expenses decreased $3.8 million for the six months ended June 30, 2015 as compared to the same period in 2014. The decrease is primarily related to lower legal fees incurred during the current period, and lower depreciation expense as certain fixed assets have been fully depreciated, partially offset by higher stock-based compensation expense related to new grants.

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Litigation settlement On April 22, 2014, the Company entered into a settlement agreement with Enzo with respect to our dispute with Enzo Life Sciences, Inc. brought in the Southern District Court of New York. Pursuant to the agreement the Company agreed to pay Enzo $5.1 million as consideration for both parties agreeing to release each other from all liabilities and claims arising under both lawsuits. As the settlement related to past claims with no ongoing benefit, these costs were recognized during the first three months of 2014 when the amount was determined to be probable and estimable.

OTHER INCOME (EXPENSE), NET

Dollars in thousands	Three Months Ended June 30,			$ Change			% Change	Six Months Ended June 30,					$ Change			% Change
	2015	2014						2015			2014
Other income (expense), net	275	$	1,418	$	(1,143	)	(81)%	$	(398	)	$	1,711	$	(2,109	)	(123)%
Interest expense	1,471	1,623		(152		)	9%	2,953			3,377		(424		)	13%

Other income (expense), net Other income (expense), net, decreased $1.1 million and $2.1 million, respectively, for the three and six months ended June 30, 2015 as compared to the same periods in 2014. The decrease is primarily due to currency losses and a gain related to the liquidation of certain investments and subsequent receipt of cash from the fund that holds our investment in non-marketable securities in the second quarter of 2014.

Interest expense Interest expense decreased $0.2 million and $0.4 million, respectively, for the three and six months ended June 30, 2015 as compared to the same periods in 2014. The decreases are due to a combination of lower outstanding borrowings in the second quarter and first half of 2015 as well as lower interest rates following the modification of our Senior Secured Credit Facility in July 2014.

INCOME TAX PROVISION

Dollars in thousands	Three Months Ended June 30,				$ Change			% Change	Six Months Ended June 30,				$ Change		% Change
	2015		2014						2015		2014
Income tax provision	$	324	$	402	$	(78	)	19%	$	1,067	$	674	$	393	(58	)%

During the three and six months ended June 30, 2015, the Company recognized an income tax expense of $0.3 million and $1.1 million, respectively. The provision for income taxes during the three and six months ended June 30, 2015 primarily consists of foreign taxes offset by a state income tax benefit upon audit closure of $0.5 million.

Due to the Company’s history of cumulative operating losses, management concluded that, after considering all the available objective evidence, it is not more likely than not that all the Company’s net deferred tax assets will be realized. Accordingly, all of the Company's U.S. deferred tax assets continue to be subject to a valuation allowance as of June 30, 2015.

As of June 30, 2015, the total amount of unrecognized tax benefits increased minimally compared to December 31, 2014. As a result of settlements of ongoing tax examinations and/or expiration of statutes of limitations without the assessment of additional income taxes, the amount of unrecognized tax benefits that could be recognized in earnings in the next 12 months could range from zero to approximately $1.7 million.

LIQUIDITY AND CAPITAL RESOURCES

Historically, we have financed our operations primarily through product sales; borrowings under credit arrangements; sales of equity and debt securities such as our 4.00% Convertible Notes and at-the-market offerings; collaborative agreements; and licensing of our technology.

Our cash outflows have generally been as follows: cash used in operating activities such as research and development programs, sales and marketing activities, compensation and benefits of our employees and other working capital needs; cash paid for acquisitions; cash paid for capital expenditures; cash paid for litigation activity and settlements; and cash used for the payment of principal on debt obligations and repurchases of our convertible notes as well as interest payments on our long-term debt obligations.

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As of June 30, 2015, we had cash and cash equivalents of approximately $119.6 million. We anticipate that our existing capital resources along with the cash to be generated from operations will enable us to maintain currently planned operations, debt repayments, and capital expenditures for the foreseeable future. These expectations are based on our current operating and financing plans, which are subject to change, and therefore we could require further funding. Factors that may cause us to require additional funding may include, but are not limited to: costs associated with defending third party claims; an adverse ruling in any of our current litigation proceedings; investments required to commercialize our products; investments required to upgrade our older product lines; a decline in cash generated by sales of our products and services; our need to establish and maintain existing and new collaboration and customer arrangements; future acquisitions or dispositions; initiation or expansion of research programs and collaborations; the costs involved in preparing, filing, prosecuting and enforcing intellectual property rights; the purchase of patent licenses; and other factors.

During the three months ended June 30, 2015, we prepaid $1.0 million of our senior secured debt with cash provided by operations. As of June 30, 2015, the carrying amount of the senior secured debt was $21.0 million.

As part of the terms of the senior secured debt agreement, we are required to meet certain financial and other negative covenants. As of June 30, 2015, we were in compliance with the amended covenants. Refer to Note 7, “Long-Term Debt Obligations”, for further details regarding our Senior Secured Credit Facility and 4.00% Convertible Notes.

From time to time, we may seek to retire, repurchase or exchange common stock or convertible notes in open market purchases, privately negotiated transactions dependent on market conditions, liquidity, and contractual obligations and other factors. We did not retire, repurchase or exchange any of our common stock or convertible notes during the three and six months ended June 30, 2015.

On November 18, 2014, we entered into a sales agreement with Cantor Fitzgerald & Co. (“Cantor Fitzgerald”) to offer shares of our common stock, $0.01 par value per share, from time to time through Cantor Fitzgerald, as our sales agent for the offer and sale of the shares. We may offer and sell shares for an aggregate offering price of up to $50.0 million. During the three months ended June 30, 2015, the Company has sold a total of 1.6 million shares of common stock at an average price of $12.41 through its “at-the-market” offering, for total net proceeds of $19.4 million. During the first half of 2015, the Company has sold a total of 3.8 million shares of common stock at an average price of $12.05 through its "at-the-market" offering, for total net proceeds of $44.7 million.

Cashflow (in thousands)

	Six Months Ended June 30,
	2015			2014
Net cash provided by operating activities	$	11,136		$	7,634
Net cash used in investing activities	(20,433		)	(768		)
Net cash provided by (used in) financing activities	49,421			(12,522		)

Operating Activities

Net cash provided by operating activities for the six months ended June 30, 2015 was comprised of net income of $11.4 million, non-cash charges of $17.4 million and a decrease of $17.7 million related to changes in operating assets and liabilities. Adjustments for non-cash expenses include depreciation and amortization expense of $10.9 million, and share-based compensation expense of $7.3 million.

Net cash provided by operating activities for the six months end June 30, 2014 was comprised of net loss of $11.4 million, non-cash charges of $26.0 million and a decrease of $7.0 million related to changes in operating assets and liabilities. Adjustments for non-cash expenses include depreciation and amortization expense of $16.5 million, amortization expense related to inventory step-up in fair value of $4.7 million, and share-based compensation expense of $6.3 million.

Investing Activities

Net cash used in investing activities for the six months ended June 30, 2015 included cash paid for an acquisition of $14.0 million, capital expenditures of $6.1 million, and purchase of technology rights of $0.3 million.

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Net cash used in investing activities for the six months ended June 30, 2014 included proceeds from sale of non-marketable securities of $2.2 million and capital expenditures of $3.0 million.

Financing Activities

Net cash provided by financing activities for the six months ended June 30, 2015 included net proceeds of $44.7 million from our at-the-market offering, and the use of $2.0 million of early payments on the outstanding principal amount of borrowings under our Term Loan agreement. Other financing activities also consisted of stock option exercise activity of $8.0 million under our employee stock plan. Cash used in paying withholding taxes in connection with issuance of stock under our employee stock plan, net of treasury shares withheld for taxes, was $2.4 million for the six months ended June 30, 2015.

Net cash used in financing activities for the six months ended June 30, 2014 included $14.5 million of early payments on the outstanding principal amount of borrowings under our Term Loan agreement.

OFF-BALANCE SHEET ARRANGEMENTS AND AGGREGATE CONTRACTUAL OBLIGATIONS

As of June 30, 2015, we had no off-balance sheet arrangements. There have been no significant changes to our aggregate contractual obligations as compared to the disclosures in Item 7 of our Annual Report on Form 10-K for the year ended December 31, 2014, except with respect to the prepayment of amounts owned under our Term Loan as discussed above.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Foreign Currency Exchange Rate Risk

We derive a portion of our revenues in foreign currencies, predominantly in Europe and Japan. In addition, a portion of our assets are held in nonfunctional currencies of our subsidiaries. We use currency forward contracts to manage a portion of the currency exposures created from our activities denominated in foreign currencies. Our hedging program is designed to reduce, but does not entirely eliminate, the impact of currency exchange rate movements. See Note 1, "Summary of Significant Accounting Policies – Derivative Instruments", in the Notes to Consolidated Financial Statements of our Annual Report on Form 10-K for the year ended December 31, 2014 for further information.

Interest Rate Risk

We are exposed to market risk from changes in interest rates on long-term obligations. We have a combination of fixed and variable rate debt. Refer to Item 7A of our Annual Report on Form 10-K for the year ended December 31, 2014. In October 2013, we refinanced $48.0 million under our Senior Secured Credit Facility. In July 2014, we entered into the Fifth Amendment, which provides, among other things, for (1) an uncommitted incremental term loan facility in an aggregate amount not to exceed $50.0 million and (2) the reduction of interest rate margins. Our interest rate risk relates primarily to U.S. dollar LIBOR-indexed borrowings.

A 100 basis point increase in interest rates on the current borrowings is not expected to have a material impact on our financial position, results of operations or cash flows since interest on our borrowings is not material to our overall financial position.

ITEM 4. CONTROLS AND PROCEDURES

(a) Disclosure controls and procedures.

Affymetrix’s management carried out an evaluation, as required by Rule 13a-15(b) of the Securities Exchange Act of 1934 (the “Exchange Act”), with the participation of our Chief Executive Officer and our Chief Financial Officer, of the effectiveness of our disclosure controls and procedures (as defined in Exchange Act Rule 13a-15(e)), as of the end of our last fiscal quarter. Based on this evaluation, our Chief Executive Officer and our Chief Financial Officer concluded that our disclosure controls and procedures were effective as of the end of the period covered by this Quarterly Report on Form 10-Q, such that the information relating to Affymetrix and its consolidated subsidiaries required to be disclosed in our Exchange Act reports filed with the SEC (i) is recorded, processed, summarized and reported within the time periods specified in SEC rules and forms, and (ii) is accumulated and communicated to Affymetrix’s management, including our Chief Executive Officer and our Chief Financial Officer, as appropriate to allow timely decisions regarding required disclosure.

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(b) Changes in internal control over financial reporting.

Affymetrix’s management carried out an evaluation, as required by Rule 13a-15(d) of the Exchange Act, with the participation of our Chief Executive Officer and our Chief Financial Officer, of changes in Affymetrix’s internal control over financial reporting. Based on this evaluation, our Chief Executive Officer and our Chief Financial Officer concluded that there were no changes in our internal control over financial reporting that occurred during the fiscal quarter covered by this report on Form 10-Q that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

Information pertaining to legal proceedings can be found in Note 9, "Legal Proceedings" to our Condensed Consolidated Financial Statements elsewhere in this Quarterly Report on Form 10-Q, and is incorporated by reference herein.

ITEM 1A. RISK FACTORS

Our business is subject to various risks, including those described in Item 1A of our Annual Report on Form 10-K for the fiscal year ended December 31, 2014, which we strongly encourage you to review. There have been no material changes from the risk factors disclosed in Item 1A of our Form 10-K.

ITEM 2. MINE SAFETY DISCLOSURES

Not applicable.

ITEM 3. OTHER INFORMATION

None.

ITEM 4. EXHIBITS

Exhibit Number	Description of Document
10.5(34)‡	Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan, as adopted effective March 9, 2000 and amended through May 13, 2015.
31.1(1)	Certification of Chief Executive Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
31.2(1)	Certification of Chief Financial Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
32(1)	Certification of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002.
EX-101.INS	XBRL Instance Document(2)
EX-101.SCH	XBRL Taxonomy Extension Schema Document(2)
EX-101.CAL	XBRL Taxonomy Extension Calculation Linkbase Document(2)
EX-101.DEF	XBRL Taxonomy Extension Definition Linkbase Document(2)
EX-101.LAB	XBRL Taxonomy Extension Label Linkbase Document(2)
EX-101.PRE	XBRL Taxonomy Extension Presentation Linkbase Document(2)

(1) Filed herewith.

(2) Pursuant to applicable securities laws and regulations, we are deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and are not subject to liability under any anti-fraud provisions of the federal securities laws as long as we have made a good faith attempt to comply with the submission requirements and promptly amend the interactive data files after becoming aware that the interactive data files fail to comply with the submission requirements. Users of this data are advised pursuant to Rule 406T of Regulation S-T that this interactive data file is deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933, is deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, and otherwise is not subject to liability under these sections.

(34) Incorporated by reference to Registrant's Registration Statement on Form S-8 as filed on May 18, 2015 (File No. 333-204271).

‡ Management contract, compensatory plan, contract or arrangement.

31

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

	By:	/s/ GAVIN WOOD
	Name:	Gavin H. J. Wood
	Title:	Executive Vice President and Chief Financial Officer
July 30, 2015
		Duly Authorized Officer and Principal Financial And Accounting Officer

32

EX-31.1

Certification of Chief Executive Officer

Pursuant to Section 302 of Sarbanes-Oxley Act of 2002

I, Frank Witney, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Affymetrix, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report, based on such evaluation; and

(d) disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

(a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

(b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

July 30, 2015	/s/ FRANK WITNEY
	Name:	Frank Witney
	Title:	Director, President and Chief Executive Officer

EX-31.2

Certification of Chief Financial Officer
Pursuant to Section 302 of Sarbanes-Oxley Act of 2002

I, Gavin Wood, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Affymetrix, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report, based on such evaluation; and

(d) disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

(a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

(b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

July 30, 2015	/s/ GAVIN WOOD
	Name:	Gavin H. J. Wood
	Title:	Executive Vice President and Chief Financial Officer

EX-32

CERTIFICATION OF CHIEF EXECUTIVE OFFICER AND CHIEF FINANCIAL OFFICER

PURSUANT TO 18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO SECTION 906 OF SARBANES-OXLEY ACT OF 2002

The certification set forth below is being submitted in connection with this Quarterly Report on Form 10-Q for the quarter ended June 30, 2015 (the "Report") for the purpose of complying with Rule 13a-14(b) or Rule 15d-14(b) of the Securities Exchange Act of 1934 (the "Exchange Act") and Section 1350 of Chapter 63 of Title 18 of the United States Code.

Each of the undersigned certifies that, to his knowledge:

1. the Report fully complies with the requirements of Section 13(a) or 15(d) of the Exchange Act; and

2. the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of Affymetrix, Inc.

July 30, 2015	/s/ FRANK WITNEY
	Name:	Frank Witney
	Title:	Director, President and Chief Executive Officer
	/S/ GAVIN WOOD
	Name:	Gavin H. J. Wood
	Title:	Executive Vice President and Chief Financial Officer

This certification accompanying the Report is not deemed filed with the Securities and Exchange Commission for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liabilities such Section, and is not to be incorporated by reference into any filing of the Company under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended (whether made before, on or after the date of the Report), irrespective of any general incorporation language contained in such filing.

XML

DERIVATIVE FINANCIAL INSTRUMENTS GAIN (LOSS) BY HEDGING RELATIONSHIP (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Derivatives in cash flow hedging relationships:
Effect of derivative instruments on statements of operations [Abstract]
Net loss recognized in OCI	$ (2,403)	$ (181)	$ (615)	$ (478)
Net gain (loss) reclassified from accumulated OCI into Revenue	884	(314)	2,669	(758)
Net loss reclassified from accumulated OCI into Other income (expense), net	0	(7)	0	(17)
Net gain recognized in Other income (expense), net	49	19	62	1
Derivatives not designated as hedging relationships:
Effect of derivative instruments on statements of operations [Abstract]
Net gain recognized in Other income (expense), net	$ 0	$ 11	$ 0	$ 12

XML

INCOME TAXES (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Income Tax Contingency [Line Items]
Income tax expense (benefit)	$ 324,000	$ 402,000	$ 1,067,000	$ 674,000
Foreign taxes offset by a state income tax benefit	500,000		500,000
Minimum [Member]
Income Tax Contingency [Line Items]
Decrease in Unrecognized Tax Benefits is Reasonably Possible	0		0
Maximum [Member]
Income Tax Contingency [Line Items]
Decrease in Unrecognized Tax Benefits is Reasonably Possible	$ 1,700,000.0		$ 1,700,000.0

XML

LONG-TERM DEBT OBLIGATIONS, TERM LOAN AND REVOLVING CREDIT FACILITY NARRATIVE (Details)			1 Months Ended	3 Months Ended	6 Months Ended
	Oct. 17, 2013 USD ($)	Jun. 25, 2012 USD ($)	Oct. 31, 2013	Jun. 30, 2015 USD ($)	Jun. 30, 2015 USD ($)	Dec. 31, 2014 USD ($)	Jul. 28, 2014 USD ($)
Debt Instrument [Line Items]
Current portion of long-term debt				$ 4,000,000	$ 4,000,000	$ 4,000,000
Interest rate at period end				3.04%	3.04%
Uncommitted incremental term loan facility capacity							$ 50,000,000
Debt-related covenants					As of June 30 2015, the Company was in compliance with the covenants.
Debt issuance cost related to term loan		$ 4,500,000
Amortization period For debt issuance cost term loan		5 years
Outstanding principal balance of term loan as of balance sheet date				$ 21,000,000	$ 21,000,000
Interest expense incurred				300,000	600,000
Outstanding balance under revolving credit facility				$ 0	$ 0
4.00% Convertible Senior Notes
Debt Instrument [Line Items]
Debt Instrument, Interest Rate, Stated Percentage				4.00%	4.00%
Base Rate [Member] | Minimum [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	1.50%
Base Rate [Member] | Maximum [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	1.75%
London Interbank Offered Rate (LIBOR) [Member] | Debt Instrument, Redemption, Period One [Member]
Debt Instrument [Line Items]
Sum of LIBOR interest period advance determination	1 month
London Interbank Offered Rate (LIBOR) [Member] | Debt Instrument, Redemption, Period Two [Member]
Debt Instrument [Line Items]
Sum of LIBOR interest period advance determination	2 months
London Interbank Offered Rate (LIBOR) [Member] | Debt Instrument, Redemption, Period Three [Member]
Debt Instrument [Line Items]
Sum of LIBOR interest period advance determination	3 months
London Interbank Offered Rate (LIBOR) [Member] | Debt Instrument, Redemption, Period Four [Member]
Debt Instrument [Line Items]
Sum of LIBOR interest period advance determination	6 months
London Interbank Offered Rate (LIBOR) [Member] | Minimum [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	2.50%
London Interbank Offered Rate (LIBOR) [Member] | Maximum [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	2.75%
Term Loan and Revolving Credit Facility [Member]
Debt Instrument [Line Items]
Face amount		$ 100,000,000.0
Term Loan [Member]
Debt Instrument [Line Items]
Debt term		5 years
Face amount		$ 85,000,000.0
Debt outstanding	$ 38,000,000
Debt issuance cost		2,500,000
Annual amortization year one				10.00%	10.00%
Amortization year two				10.00%	10.00%
Amortization year three				10.00%	10.00%
Amortization year four				10.00%	10.00%
Amortization year five and after				60.00%	60.00%
Revolving Credit Facility [Member]
Debt Instrument [Line Items]
Debt term	5 years
Face amount	$ 10,000,000.0
Original revolving credit facility		15,000,000.0
Debt outstanding	10,000,000
Refinanced Term Loan [Member]
Debt Instrument [Line Items]
Face amount	$ 38,000,000.0
Debt issuance cost		$ 800,000
Senior Secured Credit Facility [Member]
Debt Instrument [Line Items]
Minimum prepayment percentage of excess cash flow		50.00%
Minimum prepayment percentage of net cash proceeds of issuances or incurrences of debt obligations		100.00%
Minimum prepayment percentage of net proceeds of asset sales over threshold amount		100.00%
Net proceeds of asset sales threshold to trigger prepayment		$ 2,500,000
Senior Secured Credit Facility [Member] | Interest Period Option 1 [Member]
Debt Instrument [Line Items]
Term of debt used to determine interest rate			9 years
Senior Secured Credit Facility [Member] | Interest Period Option 2 [Member]
Debt Instrument [Line Items]
Term of debt used to determine interest rate			12 years
Senior Secured Credit Facility [Member] | Minimum [Member]
Debt Instrument [Line Items]
Number of days in a year used to calculate rate			365 days
Interest coverage ratio	3.5
Senior leverage ratio	1.20
Senior Secured Credit Facility [Member] | Maximum [Member]
Debt Instrument [Line Items]
Number of days in a year used to calculate rate			366 days
Senior leverage ratio	1.75
Senior Secured Credit Facility [Member] | Federal Funds Rate [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	0.50%
Senior Secured Credit Facility [Member] | London Interbank Offered Rate (LIBOR) [Member]
Debt Instrument [Line Items]
Basis spread on variable rate	1.00%
Number of days in a year used to calculate rate			360 days
Sum of LIBOR interest period	1 month

XML

SEGMENT INFORMATION, REVENUE AND GROSS PROFIT (Details) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015 USD ($)	Jun. 30, 2014 USD ($)	Jun. 30, 2015 USD ($) segment business_unit	Jun. 30, 2014 USD ($)
Segment Reporting Information [Line Items]
Number of reportable segments | segment			2
Number of business units | business_unit			4
Operating Segments [Member]
Segment Reporting Information [Line Items]
Revenue:	$ 88,966	$ 85,432	$ 177,684	$ 168,403
Gross Profit:	57,079	48,844	111,916	95,400
Operating Segments [Member] | Affymetrix Core [Member]
Segment Reporting Information [Line Items]
Revenue:	65,038	62,085	129,484	121,532
Gross Profit:	42,507	37,230	83,133	72,234
Operating Segments [Member] | eBioscience [Member]
Segment Reporting Information [Line Items]
Revenue:	23,928	23,347	48,200	46,871
Gross Profit:	$ 14,572	$ 11,614	$ 28,783	$ 23,166

XML

WARRANTIES (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2015 USD ($)
Changes in Entity's Product Warranty Liability [Abstract]
Product warranty, beginning balance	$ 912
Additions charged to cost of product sales	1,007
Repairs and replacements	(841)
Product warranty, ending balance	$ 1,078

XML

FAIR VALUE MEASUREMENTS SCHEDULE OF FAIR VALUE HIERARCHY (Details) - Fair Value, Measurements, Recurring [Member] - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative assets	$ 1,111	$ 1,258
Non-marketable securities	3,698	3,384
Total assets	4,809	4,642
Derivatives liabilities	433	0
Fair Value, Inputs, Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative assets	1,111	1,258
Total assets	1,111	1,258
Derivatives liabilities	433	0
Fair Value, Inputs, Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Non-marketable securities	3,698	3,384
Total assets	$ 3,698	$ 3,384

XML

INVENTORIES (Tables)

6 Months Ended

Jun. 30, 2015

Inventory Disclosure [Abstract]

Inventories

At June 30, 2015 and December 31, 2014, inventories, net consisted of the following (in thousands):

	June 30, 2015		December 31, 2014
Raw materials	$	11,299	$	11,461
Work-in-process	18,736		18,147
Finished goods	28,844		27,024
Total	$	58,879	$	56,632
Short-term portion	$	54,030	$	50,676
Long-term portion	$	4,849	$	5,956

XML

LONG-TERM DEBT OBLIGATIONS, CONVERTIBLE SENIOR NOTES (Details)			3 Months Ended	6 Months Ended
	Jul. 25, 2012	Jun. 25, 2012 USD ($) $ / shares shares	Jun. 30, 2015 USD ($)	Jun. 30, 2015 USD ($)
Debt Instrument [Line Items]
Debt Instrument, 4.00% Convertible, Interest Expense			$ 1,191,000	$ 2,381,000
4.00% Convertible Senior Notes
Debt Instrument [Line Items]
Senior Notes		$ 105,000,000.0	105,000,000	105,000,000
Debt Instrument, Interest Rate, Stated Percentage		4.00%
Debt issuance costs		$ 3,900,000
Net proceeds from issuance of 4.00% convertible senior notes		$ 101,100,000
Amortization period for debt issuance cost related to convertible notes		7 years
Debt Instrument, Convertible, Shares per $1,000 principal amount of 4.00% Convertible Senior Notes	170.0319
Aggregate principal amount of senior convertible notes repurchased		$ 1,000
Maximum number of shares upon conversion of the 4.00% Notes | shares		17,857,143
Debt Instrument, Convertible, Conversion Price | $ / shares		$ 5.88
Percentage of common stock above conversion price (in hundredths)		130.00%
Number of consecutive trading days within measurement period		20 days
Number of consecutive trading days on which trading price is examined for triggering of conversion		30 days
Number of trading days to trigger measurement period within date company provides notice of redemption		5 days
Percentage of Principal Amount That The Redemption Price Will Be Equal To		100.00%
Debt Instrument, 4.00% Convertible, Interest Expense			$ 1,200,000	$ 2,400,000

XML

STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE SHARE-BASED COMPENSATION EXPENSE (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Recognized share-based compensation expense [Abstract]
Total stock-based compensation expense	$ 3,224	$ 3,127	$ 7,287	$ 6,272
Costs of product sales [Member]
Recognized share-based compensation expense [Abstract]
Total stock-based compensation expense	538	660	1,232	1,197
Research and development [Member]
Recognized share-based compensation expense [Abstract]
Total stock-based compensation expense	408	637	923	1,144
Selling, general and administrative [Member]
Recognized share-based compensation expense [Abstract]
Total stock-based compensation expense	$ 2,278	$ 1,830	$ 5,132	$ 3,931

XML

DERIVATIVE FINANCIAL INSTRUMENTS SCHEDULE OF TOTAL NOTIONAL VALUES (Details) - Net Investment Hedging [Member] - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Derivative [Line Items]
Notional amount of derivative	$ 39,683	$ 21,157
Euro [Member]
Derivative [Line Items]
Notional amount of derivative	28,636	15,982
Japanese Yen [Member]
Derivative [Line Items]
Notional amount of derivative	4,960	3,391
British Pound [Member]
Derivative [Line Items]
Notional amount of derivative	$ 6,087	$ 1,784

XML

NET INCOME (LOSS) PER COMMON SHARE, SCHEDULE OF POTENTIALLY ANTIDILUTIVE SECURITIES (Details) - shares shares in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	3,632	26,822	3,462	26,778
Employee stock options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	1,841	4,540	1,796	4,540
Employee stock purchase plan [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	174	89	87	45
Restricted stock and restricted stock units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	1,617	4,336	1,579	4,336
Convertible notes [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	0	17,857	0	17,857

XML

LONG-TERM DEBT OBLIGATIONS, SCHEDULE OF DEBT (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Debt Instrument [Line Items]
Total debt	$ 125,950	$ 127,950
Less: current portion of long-term debt	4,000	4,000
Total long-term debt	121,950	123,950
Term Loan [Member]
Debt Instrument [Line Items]
Total debt	20,950	22,950
Convertible Debt [Member]
Debt Instrument [Line Items]
Total debt	$ 105,000	$ 105,000

XML

FAIR VALUE MEASUREMENTS

6 Months Ended

Jun. 30, 2015

Fair Value Disclosures [Abstract]

FAIR VALUE MEASUREMENTS

FAIR VALUE MEASUREMENTS

Financial Assets and Liabilities Measured at Fair Value on a Recurring Basis

As of June 30, 2015 and December 31, 2014, assets and liabilities measured at fair value consisted of the following (in thousands):

	June 30, 2015						December 31, 2014
	Fair Value Measurements Using Input Types						Fair Value Measurements Using Input Types
	Level 2		Level 3		Total		Level 2		Level 3		Total
Assets:
Derivative assets	$	1,111	$	—	$	1,111	$	1,258	$	—	$	1,258
Non-marketable securities	—		3,698		3,698		—		3,384		3,384
Total assets	$	1,111	$	3,698	$	4,809	$	1,258	$	3,384	$	4,642
Liabilities:
Derivatives liabilities	$	433	$	—	$	433	$	—	$	—	$	—

Derivative financial instruments

The Company's derivative financial instruments are measured at fair value on a recurring basis utilizing Level 2 inputs as determined based on review of third-party sources. The fair value of the Company's derivative assets and liabilities is determined based on the estimated consideration the Company would pay or receive to terminate these agreements on the reporting date. The derivative assets and liabilities are located in Prepaid expenses and other current assets and Accounts payable and accrued expenses, respectively, in the accompanying Condensed Consolidated Balance Sheets.

Non-Marketable Securities

The Company believes the carrying amounts of its non-marketable securities approximated their fair values at the dates presented above. These non-marketable securities consist of an investment in a limited partnership investment fund that invests in companies in the life science industry and are located in the United States. The investments were initially valued at purchase price and subsequently on the basis of inputs that market participants would use in pricing such investments. The portfolio of investments includes Level 1 publicly-traded equity securities and Level 3 equity securities and notes.

During the year ended December 31, 2014, other-than-temporary impairment charges of $0.1 million were recognized on the Company's non-marketable securities. There were no other-than-temporary impairment charges during the six months ended June 30, 2015. Net investment losses are included in Other income (expense), net in the accompanying Consolidated Statements of Operations. Depending on market conditions, the Company may incur additional charges on this investment in the future.

The following table summarizes the change in the fair value of the Company's non-marketable securities during the six months ended June 30, 2015 (in thousands).

Balance as of December 31, 2014	$	3,384
Sales	—
Realized gains	54
Unrealized gains	260
Balance as of June 30, 2015	$	3,698

Fair Value of Long-Term Debt Obligations

As further discussed in Note 7, "Long-Term Debt Obligations", the Company's long-term debt obligations are not measured at fair value on a recurring basis and are carried at amortized cost. The Company believes the fair value of the Term Loan approximates its carrying value, or amortized cost, due to the short-term nature of these obligations and the market rates of interest they bear, and therefore is classified as Level 3 of the fair value hierarchy. The fair value of the Company’s 4.00% Notes is based on quoted market prices as of the respective balance sheet date, and therefore is classified as Level 1 of the fair value hierarchy. As of June 30, 2015, the fair value of the Company’s 4.00% Notes was approximately $209.9 million.

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STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE PERFORMANCE-BASED AWARDS NARRATIVE (Details) - Jun. 30, 2015 - USD ($) $ / shares in Units, $ in Millions	Total
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized share-based compensation expense	$ 17.5
PRSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Period for recognition	3 years
Average grant date fair value (in usd per share)	$ 8.84
Outstanding (in shares)	1,085,623
PRSU's expected to vest (in shares)	977,623
Unrecognized share-based compensation expense	$ 3.4
PRSU [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period	2 years
PRSU [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period	4 years
2015 Program [Member] | PRSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Measurement period	12 months
Period for recognition	3 years
Units granted during period (in units)	243,000
Average grant date fair value (in usd per share)	$ 11.88
2015 CEO Grants [Member] | PRSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Measurement period	12 months
Units granted during period (in units)	156,023
Average grant date fair value (in usd per share)	$ 12.37

XML

SEGMENT INFORMATION (Tables)

6 Months Ended

Jun. 30, 2015

Segment Reporting [Abstract]

Schedule of Segment Reporting Information, by Segment

The following table shows revenue and gross profit by reportable operating segment for the three and six months ended June 30, 2015 and 2014 (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Revenue:
Affymetrix Core	$	65,038	$	62,085	$	129,484	$	121,532
eBioscience	23,928		23,347		48,200		46,871
Total revenue	$	88,966	$	85,432	$	177,684	$	168,403
Gross Profit:
Affymetrix Core	$	42,507	$	37,230	$	83,133	$	72,234
eBioscience	14,572		11,614		28,783		23,166
Total gross profit	$	57,079	$	48,844	$	111,916	$	95,400

XML

NET INCOME (LOSS) PER COMMON SHARE (Tables)

6 Months Ended

Jun. 30, 2015

Earnings Per Share [Abstract]

Schedule of basic and diluted earnings per share

The following table sets forth a reconciliation of basic and diluted net income (loss) per common share (in thousands except per common share amounts):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Net income (loss)	$	7,006	$	(911	)	$	11,392	$	(11,385	)
Add effect of dilutive securities:
Interest on convertible notes	1,191		—			2,381		—
Adjusted net income (loss)	$	8,197	$	(911	)	$	13,773	$	(11,385	)
Shares used in computing basic net income (loss) per common share	78,476		72,944			76,951		72,722
Add effect of dilutive securities:
Employee stock options	1,559		—			1,604		—
Employee stock purchase plan	4					3		—
Restricted stock and restricted stock units	1,566		—			1,604		—
Convertible notes	17,857		—			17,857		—
Shares used in computing diluted net income (loss) per common share	99,462		72,944			98,019		72,722
Basic net income (loss) per common share	$	0.09	$	(0.01	)	$	0.15	$	(0.16	)
Diluted net income (loss) per common share	$	0.08	$	(0.01	)	$	0.14	$	(0.16	)

Securities excluded from diluted earnings per common share on an actual outstanding basis

The potential dilutive securities excluded from diluted net income (loss) per common share were as follows (in thousands):

	Three Months Ended June 30,		Six Months Ended June 30,
	2015	2014	2015	2014
Employee stock options	1,841	4,540	1,796	4,540
Employee stock purchase plan	174	89	87	45
Restricted stock and restricted stock units	1,617	4,336	1,579	4,336
Convertible notes	—	17,857	—	17,857
Total	3,632	26,822	3,462	26,778

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RELATED PARTY TRANSACTIONS (Details)	6 Months Ended
	Jun. 30, 2015 USD ($)
Related Party Transactions [Abstract]
Minimum royalty fee from related party	$ 100,000

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INVENTORIES (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Inventories [Abstract]
Raw materials	$ 11,299	$ 11,461
Work-in-process	18,736	18,147
Finished goods	28,844	27,024
Total	58,879	56,632
Short-term portion	54,030	50,676
Long-term portion	$ 4,849	$ 5,956

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SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2015 USD ($)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Total accumulated other comprehensive income, net of tax, beginning balance	$ (612)
(Decrease)/ Increase	(4,297)
Reclassification Adjustments	(2,669)
Total accumulated other comprehensive income, net of tax, ending balance	(7,578)
Foreign currency translation adjustment [Member]
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Total accumulated other comprehensive income, net of tax, beginning balance	(2,933)
(Decrease)/ Increase	(6,612)
Reclassification Adjustments	0
Total accumulated other comprehensive income, net of tax, ending balance	(9,545)
Unrealized change in non-marketable securities [Member]
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Total accumulated other comprehensive income, net of tax, beginning balance	1,219
(Decrease)/ Increase	261
Reclassification Adjustments	0
Total accumulated other comprehensive income, net of tax, ending balance	1,480
Unrealized change in cash flow hedges [Member]
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Total accumulated other comprehensive income, net of tax, beginning balance	1,102
(Decrease)/ Increase	2,054
Reclassification Adjustments	(2,669)
Total accumulated other comprehensive income, net of tax, ending balance	$ 487

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SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES NEW ACCOUNTING PRONOUNCEMENTS (Details) $ in Millions	Jun. 30, 2015 USD ($)
Deferred Finance Costs, Net [Abstract]
Reclassification from other assets to convertible notes, net	$ 3.1

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ACQUISITION

6 Months Ended

Jun. 30, 2015

Business Combinations [Abstract]

ACQUISITION

ACQUISITION

On May 13, 2015 ("Acquisition Date"), the Company entered into an Asset Purchase Agreement with Eureka Genomics (“Eureka”), a developer of cost-effective, low- to mid-plex, high throughput genotyping assays that use next-generation sequencing (NGS) platforms for signal readout (the “Acquisition”). The Acquisition will extend the continuum of product offerings of the Company, enabling the Company to support more applications for current customers and also serve new customers.

The Acquisition was accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the tangible and intangible assets and liabilities of Eureka were recorded at their respective fair values as of the Acquisition Date, including an amount for goodwill representing the difference between the Acquisition consideration and the fair value of the net assets. The Company is in the process of determining the fair value of certain assets with the assistance of third-party specialists; thus, the June 30, 2015 reported fair values of acquired intangible assets and goodwill are provisional and subject to change.

The results of operations of the acquired Eureka business and the estimated fair values of the assets acquired and liabilities assumed have been included in the Company's condensed consolidated financial statements since the Acquisition Date. The results of operations for Eureka since the Acquisition Date are not material to the accompanying Condensed Consolidated Statement of Operations for the three and six months ended June 30, 2015.

Purchase Price

The total purchase price for Eureka was approximately $15.0 million of cash, including $14.0 million funded as of Acquisition Date through cash on hand and $1.0 million that has been held back, which is payable within 12 months of the Acquisition Date.

Fair values of assets acquired and liabilities assumed

Assets acquired and liabilities assumed were preliminarily recorded at their estimated fair values as of the Acquisition Date and include $11.2 million of identifiable intangible assets and $0.5 million of current liabilities with residual goodwill amounting to $4.3 million.

Identified intangible assets include in process research and development (“IPR&D) and customer relationships with preliminary estimated fair values of $10.4 million and $0.8 million respectively. These estimated fair values were determined using an income approach, which recognizes that the fair value of an asset is premised upon the expected receipt of future economic benefits such as earnings and cash inflows based on current sales projections and estimated direct costs. Indications of value are developed by discounting these benefits to their present worth at a discount rate that reflects the current return requirements of market participants. These assets are finite-lived intangible assets and are being amortized over their estimated useful lives ranging from ten to fifteen years.

Goodwill

The excess of Acquisition consideration over the provisional fair value of assets acquired and liabilities assumed represents goodwill. The Company believes the factors that contributed to goodwill include synergies that are specific to the Company's consolidated business, and not available to other market participants, or other companies participating in the market, and the acquisition of a talented workforce that expands the Company's expertise in low- to mid-plex, high throughput genotyping assays. The Company expects this goodwill to be deductible for tax purposes in its entirety.

Transaction costs

The Company cumulatively incurred approximately $0.3 million of Acquisition-related costs that are reported in Selling, general and administrative expense in its Condensed Consolidated Statement of Operations, of which $0.2 million and $0.3 million was recognized in the three and six months ended June 30, 2015, respectively.

Pro Forma Financial Information (Unaudited)

The following unaudited pro forma financial information presents the combined results of operations for the three and six months ended June 30, 2015 and 2014 as if the Acquisition had been completed on January 1, 2014, with adjustments to give effect to pro forma events that are directly attributable to the Acquisition. The unaudited pro forma results do not reflect any operating efficiencies or potential cost savings that may result from the consolidation of the operations of the Company and Eureka. Accordingly, these unaudited pro forma results are presented for informational purposes only and are not necessarily indicative of what the actual results of operations of the combined company would have been if the Acquisition had occurred at the beginning of the period presented, nor are they indicative of future results of operations (in thousands, except per share data):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Revenues	$	89,064	$	85,464		$	178,069	$	168,454
Net income (loss)	6,335		(1,346		)	10,676		(12,570		)
Basic earnings per share	0.08		(0.02		)	0.14		(0.17		)
Diluted earnings per share	0.08		(0.02		)	0.13		(0.17		)

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ACQUISITION (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	May. 13, 2015	Dec. 31, 2014
Acquisition [Line Items]
Intangible assets					$ 11,200
Net liabilities					500
Goodwill	$ 156,834		$ 156,834		4,300	$ 156,178
Acquisition Date			May 13, 2015
Total purchase price			$ 15,000
Cash paid			14,000
Holdback amount			1,000
Transaction costs	200		300
Revenues	89,064	$ 85,464	178,069	$ 168,454
Net income (loss)	$ 6,335	$ (1,346)	$ 10,676	$ (12,570)
Basic earnings per share (in usd per share)	$ 0.08	$ (0.02)	$ 0.14	$ (0.17)
Diluted earnings per share (in usd per share)	$ 0.08	$ (0.02)	$ 0.13	$ (0.17)
Customer Relationships [Member]
Acquisition [Line Items]
Intangible assets					800
Useful life			10 years
In Process Research and Development [Member]
Acquisition [Line Items]
Intangible assets					$ 10,400
Useful life			15 years

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STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE AT THE MARKET OFFERING NARRATIVE (Details) - USD ($) $ / shares in Units, shares in Millions	3 Months Ended	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2015	Nov. 18, 2014
Equity [Abstract]
Common stock, par value (in usd per share)	$ 0.01	$ 0.01
Aggregate amount of offer			$ 50,000,000.0
Commission percent on gross proceeds from sale of stock			3.00%
Common stock sold (in shares)	1.6	3.8
Average share price (in usd per share)	$ 12.41	$ 12.05
Net proceeds from sale of stock	$ 19,400,000	$ 44,700,000

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LEGAL PROCEEDINGS (Details) $ in Millions	3 Months Ended
	Mar. 31, 2014 USD ($)
Settled Litigation [Member] | Southern District of New York [Member]
Loss Contingencies [Line Items]
Litigation Settlement, Amount	$ 5.1

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CONDENSED CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Current assets:
Cash and cash equivalents	$ 119,597	$ 79,923
Accounts receivable, net	52,769	46,896
Inventories, net—short-term portion	54,030	50,676
Deferred tax assets—short-term portion	3,731	3,778
Prepaid expenses and other current assets	9,065	9,197
Total current assets	239,192	190,470
Property and equipment, net	20,861	18,087
Inventories, net—long-term portion	4,849	5,956
Goodwill	156,834	156,178
Intangible assets, net	107,920	106,183
Deferred tax assets—long-term portion	297	303
Other long-term assets	8,417	9,371
Total assets	538,370	486,548
Current liabilities:
Accounts payable and accrued liabilities	45,882	53,063
Current portion of long-term debt	4,000	4,000
Deferred revenue—short-term portion	8,128	9,210
Total current liabilities	58,010	66,273
Deferred revenue—long-term portion	2,348	2,372
Convertible notes	105,000	105,000
Term loan—long-term portion	16,950	18,950
Other long-term liabilities	20,601	21,626
Total liabilities	202,909	214,221
Stockholders’ equity:
Common stock	798	743
Additional paid-in capital	840,400	781,747
Accumulated other comprehensive loss	(7,578)	(612)
Accumulated deficit	(498,159)	(509,551)
Total stockholders’ equity	335,461	272,327
Total liabilities and stockholders’ equity	$ 538,370	$ 486,548

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INVENTORIES, FAIR VALUE STEP-UP IN BASIS (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Inventory Disclosure [Abstract]
Amortization of inventory step-up in fair value	$ 0	$ 4,666

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:
Net income (loss)	$ 11,392	$ (11,385)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization	10,855	16,521
Amortization of inventory step-up in fair value	0	4,666
Share-based compensation	7,287	6,272
Deferred tax, net	(818)	(570)
Gain on sales of securities	(54)	(1,240)
Other non-cash transactions	130	356
Changes in operating assets and liabilities:
Accounts receivable, net	(5,839)	1,339
Inventories	(3,132)	(1,207)
Prepaid expenses and other assets	639	1,883
Accounts payable and accrued liabilities	(8,423)	(2,599)
Deferred revenue	(1,401)	(6,136)
Other long-term liabilities	500	(266)
Net cash provided by operating activities	11,136	7,634
CASH FLOWS FROM INVESTING ACTIVITIES:
Acquisition of business	(14,000)	0
Proceeds from sales of securities	0	2,162
Proceeds on sale of fixed assets	0	106
Capital expenditures	(6,092)	(3,036)
Purchase of technology rights	(341)	0
Net cash used in investing activities	(20,433)	(768)
CASH FLOWS FROM FINANCING ACTIVITIES:
Issuance of common stock, net of issuance costs	51,421	1,978
Repayments of long-term debt	(2,000)	(14,500)
Net cash provided by (used in) financing activities	49,421	(12,522)
Effect of exchange rate changes on cash and cash equivalents	(450)	28
Net increase (decrease) in cash and cash equivalents	39,674	(5,628)
Cash and cash equivalents at beginning of period	79,923	57,128
Cash and cash equivalents at end of period	$ 119,597	$ 51,500

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FAIR VALUE MEASUREMENTS CHANGES IN FAIR VALUE MEASUREMENT OF LEVEL 3 ITEMS (Details) - Fair Value, Measurements, Recurring [Member] $ in Thousands	6 Months Ended
	Jun. 30, 2015 USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance as of December 31, 2014	$ 3,384
Balance as of June 30, 2015	3,698
Fair Value, Inputs, Level 3 [Member]
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance as of December 31, 2014	3,384
Sales	0
Realized gains	54
Unrealized gains	260
Balance as of June 30, 2015	$ 3,698

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FAIR VALUE MEASUREMENTS (Tables)

6 Months Ended

Jun. 30, 2015

Fair Value Disclosures [Abstract]

Financial assets and liabilities measured at fair value on a recurring basis

As of June 30, 2015 and December 31, 2014, assets and liabilities measured at fair value consisted of the following (in thousands):

	June 30, 2015						December 31, 2014
	Fair Value Measurements Using Input Types						Fair Value Measurements Using Input Types
	Level 2		Level 3		Total		Level 2		Level 3		Total
Assets:
Derivative assets	$	1,111	$	—	$	1,111	$	1,258	$	—	$	1,258
Non-marketable securities	—		3,698		3,698		—		3,384		3,384
Total assets	$	1,111	$	3,698	$	4,809	$	1,258	$	3,384	$	4,642
Liabilities:
Derivatives liabilities	$	433	$	—	$	433	$	—	$	—	$	—

Fair value of non-marketable securities

The following table summarizes the change in the fair value of the Company's non-marketable securities during the six months ended June 30, 2015 (in thousands).

Balance as of December 31, 2014	$	3,384
Sales	—
Realized gains	54
Unrealized gains	260
Balance as of June 30, 2015	$	3,698

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DERIVATIVE FINANCIAL INSTRUMENTS (Details) - Jun. 30, 2015 - USD ($) $ in Millions	Total
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Expected deferred loss amount to be recognized in OCI	$ 0.5
Maximum expected period to recognized deferred amount into earnings	12 months

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STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE (Tables)

6 Months Ended

Jun. 30, 2015

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Share-based compensation expense

The Company recognized share-based compensation expense in the accompanying Condensed Consolidated Statements of Operations for the three and six months ended June 30, 2015 and 2014, as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Costs of product sales	$	538	$	660	$	1,232	$	1,197
Research and development	408		637		923		1,144
Selling, general and administrative	2,278		1,830		5,132		3,931
Total share-based compensation expense	$	3,224	$	3,127	$	7,287	$	6,272

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SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

6 Months Ended

Jun. 30, 2015

Accounting Policies [Abstract]

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles ("GAAP") for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited condensed consolidated financial statements include the accounts of Affymetrix, Inc. and its wholly-owned subsidiaries (“Affymetrix” or the “Company”). All significant intercompany accounts and transactions have been eliminated in consolidation. In the opinion of management, all adjustments, consisting of normal recurring entries, considered necessary for a fair presentation have been included.

Interim financial results are not necessarily indicative of results anticipated for the full year. These unaudited financial statements should be read in conjunction with the Company's audited financial statements and footnotes included in the Company's Annual Report on Form 10-K for the year ended December 31, 2014, from which the balance sheet information as of that date and as included herein was derived.

The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, and expenses, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.

There have been no material changes to the Company’s significant accounting policies as compared to the significant accounting policies described in the Company’s Annual Report on Form 10-K for the year ended December 31, 2014.

Comprehensive Income (Loss)

Comprehensive income (loss) is comprised of net income (loss) and other comprehensive income (loss) (“OCI”). OCI includes foreign currency translation adjustments, unrealized gains and losses on the Company's non-marketable securities and unrealized gains and losses on cash flow hedges that are excluded from net income (loss). Total comprehensive income (loss) has been disclosed in the Company's Condensed Consolidated Statements of Comprehensive Income (Loss).

The following table summarizes the amounts reclassified out of accumulated other comprehensive loss, net of tax, for the six months ended June 30, 2015 (in thousands):

	December 31, 2014			(Decrease)/ Increase			Reclassification Adjustments			June 30, 2015
Foreign currency translation adjustment	$	(2,933	)	$	(6,612	)	$	—		$	(9,545	)
Unrealized change in non-marketable securities	1,219			261			—			1,480
Unrealized change in cash flow hedges	1,102			2,054			(2,669		)	487
Total accumulated other comprehensive loss, net of tax	$	(612	)	$	(4,297	)	$	(2,669	)	$	(7,578	)

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2014-09, Revenue from Contracts with Customers (ASU 2014-09) to provide guidance on revenue recognition. ASU 2014-09 requires a company to recognize revenue when it transfers promised goods or services to customers in an amount that reflects the consideration to which the company expects to be entitled in exchange for those goods or services. In doing so, companies will need to use more judgment and make more estimates than under today’s guidance. These may include identifying performance obligations in the contract, estimating the amount of variable consideration to include in the transaction price and allocating the transaction price to each separate performance obligation. In April 2015, the FASB proposed a one-year deferral of the effective date for ASU 2014-09. Under the proposal, ASU 2014-09 is effective for the Company in the first quarter of 2018. Early adoption up to the first quarter of 2017 is permitted. Upon adoption, ASU 2014-09 can be applied retrospectively to all periods presented or only to the most current period presented with the cumulative effect of changes reflected in the opening balance of retained earnings in the most current period presented. The Company is currently evaluating the method of adoption and the impact of adopting ASU 2014-09 on its consolidated financial statements.

In May 2015, the FASB issued Accounting Standards Update No. 2015-03, Interest - Imputation of Interest (ASU 2015-03) to provide guidance on the presentation of debt issuance costs. ASU 2015-03 requires a company to present debt issuance costs as a reduction from the carrying amount of the financial liability and not recorded as separate assets. ASU 2015-03 is effective for the Company in the first quarter of 2016. Early adoption is permitted. Upon adoption, ASU 2015-03 should be applied retrospectively to all periods presented. The Company's adoption of ASU 2015-03 would have resulted in a decrease in Other long-term assets, Convertible notes, and Term loan—long-term portion of $3.1 million as of June 30, 2015.

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CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
REVENUE:
Product sales	$ 79,897	$ 75,880	$ 159,265	$ 149,576
Services and other	9,069	9,552	18,419	18,827
Total revenue	88,966	85,432	177,684	168,403
COSTS AND EXPENSES:
Cost of product sales	27,156	30,560	54,741	60,071
Cost of services and other	4,731	6,028	11,027	12,932
Research and development	12,911	12,882	25,032	24,517
Selling, general and administrative	35,642	36,266	71,074	74,828
Litigation settlement	0	0	0	5,100
Total costs and expenses	80,440	85,736	161,874	177,448
Income (loss) from operations	8,526	(304)	15,810	(9,045)
Other income (expense), net	275	1,418	(398)	1,711
Interest expense	1,471	1,623	2,953	3,377
Income (loss) before income taxes	7,330	(509)	12,459	(10,711)
Income tax provision	324	402	1,067	674
Net income (loss)	$ 7,006	$ (911)	$ 11,392	$ (11,385)
Basic net income (loss) per common share (in usd per share)	$ 0.09	$ (0.01)	$ 0.15	$ (0.16)
Diluted net income (loss) per common share (in usd per share)	$ 0.08	$ (0.01)	$ 0.14	$ (0.16)
Shares used in computing basic net income (loss) per common share (in shares)	78,476	72,944	76,951	72,722
Shares used in computing diluted net income (loss) per common share (in shares)	99,462	72,944	98,019	72,722

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INCOME TAXES

6 Months Ended

Jun. 30, 2015

Income Tax Disclosure [Abstract]

INCOME TAXES

INCOME TAXES

During the three and six months ended June 30, 2015, the Company recognized income tax expense of $0.3 million and $1.1 million, respectively. The provision for income taxes during the three and six months ended June 30, 2015 primarily consists of foreign taxes offset by a state income tax benefit upon audit closure of $0.5 million.

Due to the Company’s history of cumulative operating losses, management concluded that, after considering all the available objective evidence, it is not more likely than not that all the Company’s net deferred tax assets will be realized. Accordingly, all of the Company's U.S. deferred tax assets continue to be subject to a valuation allowance as of June 30, 2015.

As of June 30, 2015, the total amount of unrecognized tax benefits increased minimally compared to December 31, 2014. As a result of settlements of ongoing tax examinations and/or expiration of statues of limitations without the assessment of additional income taxes, the amount of unrecognized tax benefits that could be recognized in earnings in the next 12 months could range from zero to approximately $1.7 million.

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Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2015	Jul. 27, 2015
Document and Entity Information [Abstract]
Entity Registrant Name	AFFYMETRIX INC
Entity Central Index Key	0000913077
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2015
Document Fiscal Year Focus	2015
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		79,820,002

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SEGMENT INFORMATION

6 Months Ended

Jun. 30, 2015

Segment Reporting [Abstract]

SEGMENT INFORMATION

SEGMENT INFORMATION

The Company reports segment information on the "management" approach which designates the internal reporting used by management for making decisions and assessing performance as the source of the Company's reportable segments. The Company's chief operating decision maker ("CODM") is responsible for reviewing and approving investments in the Company's technology platforms and manufacturing infrastructure. The Company is organized into two reportable segments: Affymetrix Core and eBioscience.

Affymetrix Core is divided into four business units, with each business unit having its own strategic marketing and research and development groups to better serve customers and respond quickly to market needs. Affymetrix Core manufacturing operations are based on platforms that are used to produce various Affymetrix Core products that serve multiple applications and markets and similar customer and economic characteristics. Additionally, the business units share certain research, development, commercial operations and common corporate services that provide capital, infrastructure and functional support. As such, the Company concluded that the four business units represent one reportable operating segment. The following describes the four business units that form Affymetrix Core:

• Expression: This business unit markets the Company's GeneChip® gene expression products and services;

• Genetic Analysis and Clinical Applications: This business unit markets the Company's Axiom® genotyping product line, as well as products with clinical diagnostic and research applications including CytoScan® products, OncoScan® products, and the ViewRNA® in situ tissue hybridization platform for clinical translational research. In addition, the business unit is responsible for managing the Powered by Affymetrix™ (PbA) clinical partnering and licensing program which enables third-party diagnostic companies to access and develop DNA and RNA-based diagnostic tests based on Affymetrix technology platforms. This business unit also markets the CytoScan® Dx product, the recently FDA cleared microarray system as an aid for the post-natal diagnosis of children with developmental delays and intellectual disabilities;

• Life Science Reagents: This business unit sells reagents, enzymes, purification kits and biochemicals used by life science researchers and other biological and health care manufacturers, including those developing and marketing Next Generation Sequencing (“NGS”) products and molecular diagnostics; and

• Corporate: This business unit is comprised primarily of incidental revenue from royalty arrangements and field revenue from field-services provided to customers of the Company.

The eBioscience business unit operates with its own manufacturing, research and development, and marketing groups. The business unit does utilize certain Corporate functions such as finance, legal, commercial operations and human resources. This reportable segment specializes in the areas of flow cytometry reagents, immunoassays, microscopic imaging, other protein-based analyses, QuantiGene® single and multiplex RNA solution assays (not including the View RNA in situ tissue hybridization platform) and the ProcartaPlex™ multiplex immunoassay product lines.

All business units sell their products through the Global Commercial Organization comprised of sales, field application and engineering support personnel. The Company markets and distributes its products directly to customers in North America, Japan and major European markets. In these markets, the Company has its own sales, service and application support personnel responsible for expanding and managing their respective customer bases. In other markets, such as Mexico, India, Brazil, the Middle East and Asia Pacific, including China, the Company sells its products principally through third-party distributors that specialize in life science supply. The Company is selectively expanding its presence in the larger and more attractive markets, such as China. For certain molecular diagnostic and industrial opportunities, the Company supplies its partners with arrays and instruments, which they incorporate into diagnostic products or other routine applications and assume the primary commercialization responsibilities.

During 2015, the commercial organization and general and administrative functions are fully integrated. The Company no longer reports these operating expenses at a segment level and began evaluating the performance of its reportable segments based on revenue and gross profit. Revenue is allocated to each business unit based on product codes. The 2014 amounts have been recast to conform to the current presentation.

The following table shows revenue and gross profit by reportable operating segment for the three and six months ended June 30, 2015 and 2014 (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Revenue:
Affymetrix Core	$	65,038	$	62,085	$	129,484	$	121,532
eBioscience	23,928		23,347		48,200		46,871
Total revenue	$	88,966	$	85,432	$	177,684	$	168,403
Gross Profit:
Affymetrix Core	$	42,507	$	37,230	$	83,133	$	72,234
eBioscience	14,572		11,614		28,783		23,166
Total gross profit	$	57,079	$	48,844	$	111,916	$	95,400

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CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Statement of Comprehensive Income [Abstract]
Net income (loss)	$ 7,006	$ (911)	$ 11,392	$ (11,385)
Other comprehensive income (loss), net of tax:
Foreign currency translation adjustment	1,510	(609)	(6,612)	(458)
Unrealized change in available-for-sale and non-marketable securities (net of $0 tax for the three and six months ended June 30, 2015, respectively; net of tax of $(545) and $256 for the three and six months ended June 30, 2014, respectively)	37	(898)	261	421
Unrealized change in cash flow hedges (net of $0 tax for the three and six months ended June 30, 2015 and 2014)	(2,403)	181	(615)	478
Net change in other comprehensive income (loss), net of tax	(856)	(1,326)	(6,966)	441
Comprehensive income (loss)	$ 6,150	$ (2,237)	$ 4,426	$ (10,944)

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INVENTORIES

6 Months Ended

Jun. 30, 2015

Inventory Disclosure [Abstract]

INVENTORIES

INVENTORIES

At June 30, 2015 and December 31, 2014, inventories, net consisted of the following (in thousands):

	June 30, 2015		December 31, 2014
Raw materials	$	11,299	$	11,461
Work-in-process	18,736		18,147
Finished goods	28,844		27,024
Total	$	58,879	$	56,632
Short-term portion	$	54,030	$	50,676
Long-term portion	$	4,849	$	5,956

During the six months ended June 30, 2014, amortization expense was approximately $4.7 million related to the fair value step-up of inventory acquired from eBioscience. The inventory fair value step-up was fully amortized as of June 30, 2014.

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STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE

6 Months Ended

Jun. 30, 2015

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE

STOCKHOLDERS’ EQUITY AND SHARE-BASED COMPENSATION EXPENSE

At the Market Offering

On November 18, 2014, the Company entered into a sales agreement with Cantor Fitzgerald & Co. (“Cantor Fitzgerald”) to offer shares of its common stock, $0.01 par value per share, from time to time through Cantor Fitzgerald, as the Company’s sales agent for the offer and sale of the shares. The Company may offer and sell shares for an aggregate offering price of up to $50.0 million. The Company pays a commission equal to 3% of the gross proceeds from the sale of shares of its common stock under the sales agreement. The Company intends to use the net proceeds from this offering for general corporate purposes, including capital expenditures, debt repayments and working capital. The Company may also use a portion of the net proceeds from this offering to acquire or invest in complementary businesses, technologies, product candidates or other intellectual property, although there are no present commitments or agreements to do so. The Company is not obligated to make any sales of shares of common stock under the sales agreement. During the three months ended June 30, 2015, the Company sold a total of 1.6 million shares of common stock at an average price of $12.41 through its “at-the-market” offering, for total net proceeds of $19.4 million. During the first half of 2015, the Company sold a total of 3.8 million shares of common stock at an average price of $12.05 through its "at-the-market" offering, for total net proceeds of $44.7 million.

Share-based Compensation Plans

The Company has a share-based compensation program, most recently the 2000 Amended and Restated Equity Incentive Plan (the “Plan”), that provides the Board of Directors broad discretion in creating equity incentives for employees, officers, directors and consultants. This program includes incentive and non-qualified stock options and non-vested stock awards (also known as restricted stock) granted under various stock plans. As of June 30, 2015, the Company had approximately 6.6 million shares of common stock reserved for future issuance under its share-based compensation plans. New shares are issued as a result of stock option exercises, restricted stock units vesting and restricted stock award grants.

The Company recognized share-based compensation expense in the accompanying Condensed Consolidated Statements of Operations for the three and six months ended June 30, 2015 and 2014, as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2015		2014		2015		2014
Costs of product sales	$	538	$	660	$	1,232	$	1,197
Research and development	408		637		923		1,144
Selling, general and administrative	2,278		1,830		5,132		3,931
Total share-based compensation expense	$	3,224	$	3,127	$	7,287	$	6,272

As of June 30, 2015, $17.5 million of total unrecognized share-based compensation expense related to non-vested awards is expected to be recognized over the respective vesting terms of each award through 2018. The weighted‑average terms of the unrecognized share-based compensation expense are 2.1 years for stock options and 1.9 years for restricted stock.

Performance-Based Awards

The Company's share-based awards program includes performance-based restricted stock awards ("PRSUs") that vest based upon the achievement of certain performance criteria and a service vesting criteria following the achievement of performance criteria. Performance criteria include various operational criteria of the Company such as revenues, earnings before interest, taxes, depreciation and amortization, earnings per share, and similar criteria, either on a Company-wide or business unit specific basis. The service vesting criteria ranges from two to four years. The Company recognizes the fair value of these awards to the extent the achievement of the related performance criteria is estimated to be probable. If a performance criteria is subsequently determined to not be probable of achievement, any related expense is reversed in the period such determination is made. Conversely, if a performance criteria is not currently expected to be achieved but is later determined to be probable of achievement, a “catch-up” entry is recorded in the period such determination is made for the expense that would have been recognized had the performance criteria been probable of achievement since the grant of the award.

2015 Program During the first quarter of 2015, the Compensation Committee granted certain PRSUs associated with performance criteria referred to as the 2015 Program. The purpose of the 2015 Program is to retain key employees. The measurement period for the 2015 Program is the twelve month period ending December 31, 2015 and the awards granted under the 2015 Program were granted in the form of performance shares pursuant to the terms of our 2000 Plan. Based on the achievement of the performance conditions, shares of stock would vest in equal installments over three years. The level of achievement of 2015 financial performance will be assessed during the first quarter of 2016 after which the shares of stock will be issued to the participants, contingent upon the recipient’s continued service to the Company. In 2015, the Company awarded 243,000 PRSUs under the 2015 Program at a grant date fair value of $11.88 per PRSU.

2015 CEO Grants During the second quarter of 2015, the Board of Directors approved a grant of PRSUs associated with performance criteria to the Company's Chief Executive Officer ("CEO") referred to as the 2015 CEO Grant. The measurement period for the 2015 CEO Grant is the twelve month period ending December 31, 2017 and the awards granted under the 2015 CEO Grant were granted in the form of performance shares pursuant to the terms of our 2000 Plan. The 2015 CEO Grant entitles the CEO to receive a certain number of shares of the Company's common stock based on the Company's satisfaction of certain financial performance goals as set and approved by the Board of Directors during the current quarter. Based on the achievement of the performance conditions during the Performance Period, the final settlement of the PRSU award will vest in February 2018. The level of achievement of 2017 financial performance will be assessed during the first quarter of 2018. The PRSU award will be forfeited if the performance goals are not met or if the CEO is no longer employed at the vest date. The Company awarded 156,023 PRSUs under the 2015 CEO Grant at a grant date fair value of $12.37 per PRSU.

As of June 30, 2015, there were 1,085,623 company-wide PRSUs outstanding with an average grant date fair value of $8.84 per PRSU. The Company expects that it is probable that 977,623 of these PRSUs will vest and that the related unrecognized stock compensation expense of $3.4 million will be recognized over the next three years. Changes in the Company’s assessment of the probability of achievement of performance criteria could have a material effect on the results of operations in future periods. There were no material changes in estimate related to the probability of vesting or recognition of expense related to PRSUs during either of the periods ended June 30, 2015 or 2014.

For additional information concerning the Company's share-based compensation plans, including performance-based awards programs, see Note 13, "Stockholders' Equity and Share-Based Compensation Expense", to the consolidated financial statements in Part II, Item 8 of the Company's 2014 Annual Report on Form 10-K.

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DERIVATIVE FINANCIAL INSTRUMENTS (Tables)

6 Months Ended

Jun. 30, 2015

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Notional values of entity's foreign currency forward contracts mature within 12 months

As of June 30, 2015 and December 31, 2014, the total notional values of the Company’s derivative assets and liabilities were as follows (in thousands):

	June 30, 2015		December 31, 2014
Euro	$	28,636	$	15,982
Japanese Yen	4,960		3,391
British Pound	6,087		1,784
Total	$	39,683	$	21,157

Entity's foreign currency derivatives measured at fair value

The Company records all derivative assets and liabilities on the accompanying Condensed Consolidated Balance sheets at fair value. The following table shows the Company’s derivatives as of June 30, 2015 and December 31, 2014 (in thousands):

	June 30, 2015		December 31, 2014		Balance Sheet Classification
Derivative assets:
Foreign exchange contracts	$	1,111	$	1,258	Prepaid expenses and other current assets
Derivative liabilities:
Foreign exchange contracts	433		—		Accounts payable and accrued liabilities

Effect of entity's derivative instruments, net of tax, on Condensed Statements of Operations

The following table shows the effect, net of tax, of the Company’s derivative instruments on the accompanying Condensed Consolidated Statements of Operations and OCI for the three and sixmonths endedJune 30, 2015and 2014 (in thousands):

	Three Months Ended   June 30,						Six Months Ended   June 30,
	2015			2014			2015			2014
Derivatives in cash flow hedging relationships:
Net loss recognized in OCI	$	(2,403	)	$	(181	)	$	(615	)	$	(478	)
Net gain (loss) reclassified from accumulated OCI into Revenue	884			(314		)	2,669			(758		)
Net loss reclassified from accumulated OCI into Other income (expense), net	—			(7		)	—			(17		)
Net gain recognized in Other income (expense), net	49			19			62			1
Derivatives not designated as hedging relationships:
Net gain recognized in Other income (expense), net	—			11			—			12

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RELATED PARTY TRANSACTIONS

6 Months Ended

Jun. 30, 2015

Related Party Transactions [Abstract]

RELATED PARTY TRANSACTIONS

RELATED PARTY TRANSACTIONS

In December 2011, the Company entered into an agreement under which it assigned one patent application and related know-how to Cellular Research, Inc. (“Cellular Research”), a company founded by the Company’s former Chairman, Dr. Stephen P.A. Fodor. Dr. Fodor also owns a majority of the shares of Cellular Research. Pursuant to the agreement, Cellular Research shall pay single digit royalties to Affymetrix on sales of products covered by the assigned technology, and starting in December 2016, an annual minimum fee of $100,000. Affymetrix shall also have a right of first refusal to collaborate with Cellular Research for the development of certain new products and to supply arrays to Cellular Research under certain terms and conditions. As of June 30, 2015, no significant royalties have been earned from this agreement.

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NET INCOME (LOSS) PER COMMON SHARE

6 Months Ended

Jun. 30, 2015

Earnings Per Share [Abstract]

NET INCOME (LOSS) PER COMMON SHARE

NET INCOME (LOSS) PER COMMON SHARE

Basic earnings per common share is calculated using the weighted‑average number of common shares outstanding during the period less the weighted‑average shares subject to repurchase. Diluted earnings per common share gives effect to dilutive common stock subject to repurchase, stock options (calculated based on the treasury stock method), shares purchased under the employee stock purchase plan and convertible debt (calculated using an as-if-converted method).

The following table sets forth a reconciliation of basic and diluted net income (loss) per common share (in thousands except per common share amounts):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Net income (loss)	$	7,006	$	(911	)	$	11,392	$	(11,385	)
Add effect of dilutive securities:
Interest on convertible notes	1,191		—			2,381		—
Adjusted net income (loss)	$	8,197	$	(911	)	$	13,773	$	(11,385	)
Shares used in computing basic net income (loss) per common share	78,476		72,944			76,951		72,722
Add effect of dilutive securities:
Employee stock options	1,559		—			1,604		—
Employee stock purchase plan	4					3		—
Restricted stock and restricted stock units	1,566		—			1,604		—
Convertible notes	17,857		—			17,857		—
Shares used in computing diluted net income (loss) per common share	99,462		72,944			98,019		72,722
Basic net income (loss) per common share	$	0.09	$	(0.01	)	$	0.15	$	(0.16	)
Diluted net income (loss) per common share	$	0.08	$	(0.01	)	$	0.14	$	(0.16	)

The potential dilutive securities excluded from diluted net income (loss) per common share were as follows (in thousands):

	Three Months Ended June 30,		Six Months Ended June 30,
	2015	2014	2015	2014
Employee stock options	1,841	4,540	1,796	4,540
Employee stock purchase plan	174	89	87	45
Restricted stock and restricted stock units	1,617	4,336	1,579	4,336
Convertible notes	—	17,857	—	17,857
Total	3,632	26,822	3,462	26,778

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WARRANTIES

6 Months Ended

Jun. 30, 2015

Product Warranties Disclosures [Abstract]

WARRANTIES

WARRANTIES

The Company provides for anticipated warranty costs at the time the associated product revenue is recognized. Accrued warranties are included in Accounts payable and accrued liabilities in the accompanying Condensed Consolidated Balance Sheets. Product warranty costs are estimated based upon the Company’s historical experience and the applicable warranty period. The Company periodically reviews the adequacy of its warranty reserve and adjusts, if necessary, the warranty percentage and accrual based on actual experience and estimated costs to be incurred. Changes to the Company’s product warranty liability for the six months ended June 30, 2015 are as follows (in thousands):

Balance at December 31, 2014	$	912
Additions charged to cost of product sales	1,007
Repairs and replacements	(841		)
Balance at June 30, 2015	$	1,078

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LONG-TERM DEBT OBLIGATIONS

6 Months Ended

Jun. 30, 2015

Debt Disclosure [Abstract]

LONG-TERM DEBT OBLIGATIONS

LONG-TERM DEBT OBLIGATIONS

The following table summarizes the carrying amount of the Company's borrowings (in thousands):

	June 30, 2015		December 31, 2014
Term loan	$	20,950	$	22,950
Convertible notes	105,000		105,000
Total debt	125,950		127,950
Less: current portion of long-term debt	4,000		4,000
Total long-term debt	$	121,950	$	123,950

Term Loan and Revolving Credit Facility

On June 25, 2012, in conjunction with the acquisition of eBioscience, Inc., the Company entered into a five year $100.0 million Senior Secured Credit Facility credit agreement (the “Credit Agreement”). The Credit Agreement provided for a Term Loan in an aggregate principal amount of $85.0 million and a revolving credit facility in an aggregate principal amount of $15.0 million.

On October 17, 2013, the Company refinanced its Senior Secured Credit Facility and entered into the Fourth Amendment to Credit Agreement (the "Fourth Amendment"). The Fourth Amendment provided, among other things, for a term loan in the aggregate principal amount of $38.0 million and revolving loan commitments in the aggregate principal amount of $10.0 million, each with a term of five years. The Company borrowed a total of $38.0 million under the Term Loan and $10.0 million under the revolving loan upon refinancing.

On July 28, 2014, the Company entered into the Fifth Amendment to Credit Agreement (the "Fifth Amendment" and the Credit Agreement as so amended, the "Amended Credit Agreement"). The Fifth Amendment provides, among other things, for (1) an uncommitted incremental term loan facility in an aggregate amount not to exceed $50.0 million and (2) the reduction of interest rate margins. As of June 30, 2015, the applicable interest rate was approximately 3.04%.

At the option of the Company (subject to certain limitations), borrowings under the Amended Credit Agreement bear interest at either a base rate or at the London Interbank Offered Rate (“LIBOR”), plus, in each case, an applicable margin. Under the Base Rate Option, interest will be at the base rate plus 1.5% to 1.75% dependent on the senior leverage ratio then in effect calculated on the basis of the actual number of days elapsed in a year of 365 or 366 days (as applicable) and payable quarterly in arrears. The base rate will be equal to the greatest of (a) the rate last quoted by The Wall Street Journal (or another national publication described in the Amended Credit Agreement) as the U.S. “Prime Rate,” (b) the federal funds rate, plus 0.50% per annum or (c) LIBOR for an interest period of one month, plus 1.00% per annum. Under the LIBOR Option, interest will be determined based on interest periods to be selected by Affymetrix of one, two, three or six months (and, to the extent available to all relevant lenders, nine or 12 years) and will be equal to LIBOR plus 2.50% and 2.75% dependent on the senior leverage ratio then in effect, calculated based on the actual number of days elapsed in a 360-day year. Interest will be paid at the end of each interest period or in the case of interest periods longer than three months, quarterly.

The loans and other obligations under the Senior Secured Credit Facility are (i) guaranteed by substantially all of the Company’s domestic subsidiaries (subject to certain exceptions and limitations) and (ii) secured by substantially all of the assets of Affymetrix and each guarantor (subject to certain exceptions and limitations).

The Amended Credit Agreement requires the Company to maintain an interest coverage ratio of at least 3.5 to 1.0 and a senior leverage ratio not exceeding initially 1.75 to 1.00 and stepping down to 1.20 to 1.00. The Amended Credit Agreement also includes other covenants, including negative covenants that, subject to certain exceptions, limit Affymetrix’, and that of certain of its subsidiaries’, ability to, among other things: (i) incur additional debt, including guarantees by the Company or its subsidiaries, (ii) make investments, pay dividends on capital stock, redeem or repurchase capital stock, redeem or repurchase the Company’s senior convertible notes or any subordinated obligations, (iii) create liens and negative pledges, (iv) make capital expenditures, (v) dispose of assets, (vi) make acquisitions, (vii) create or permit restrictions on the ability of Affymetrix’ subsidiaries to pay dividends or make distributions to Affymetrix, (viii) engage in transactions with affiliates, (ix) engage in sale and leaseback transactions, (x) consolidate or merge with or into other companies or sell all or substantially all the Company’s assets and (xi) change their nature of business, their organizational documents or their accounting policies.

The Company is required to make the following mandatory prepayments: (a) annual prepayments in an amount equal to 50% of excess cash flow (as defined in the Amended Credit Agreement), subject to leverage-based step-downs, (b) prepayments in an amount equal to 100% of the net cash proceeds of issuances or incurrences of debt obligations of Affymetrix and its subsidiaries (other than debt incurrences expressly permitted by the Credit Agreement), (c) prepayments in an amount equal to 100% of the net proceeds of asset sales in excess of $2.5 million annually (subject to certain reinvestment rights) and (d) prepayments in an amount equal to any indemnification payments or similar payments received under the Acquisition Agreement, subject to certain exclusions.

The Amended Credit Agreement also contains events of default, including payment defaults, breaches of representations and warranties, covenant defaults, cross-default and cross-acceleration to other indebtedness in excess of specified amounts, monetary judgment defaults in excess of specified amounts, bankruptcy or insolvency, actual or asserted invalidity or impairment of any part of the credit documentation (including the failure of any lien on a material portion of the collateral to remain perfected) and change of ownership or control defaults. In addition, the occurrence of a “fundamental change” under the indenture governing the 4.00% Convertible Notes would be an event of default under the Amended Credit Agreement. As of June 30 2015, the Company was in compliance with the covenants.

The proceeds received on June 25, 2012 from the original Term Loan were net of debt issuance costs of approximately $4.5 million being amortized over the 5-year term of the Senior Secured Credit Facility. Following the refinancing under the Fourth Amendment, the Company wrote off unamortized debt issuance costs of $2.5 million associated with the original Term Loan, and received proceeds on October 17, 2013 from the new Term Loan and Revolver, net of debt issuance costs of approximately $0.8 million that amortize on the effective interest rate method beginning October 17, 2013.

As of June 30, 2015, the Company had an outstanding principal balance of approximately $21.0 million under the Term Loan and incurred $0.3 million and $0.6 million in interest expense under the Senior Secured Credit Facility for the three and six months ended June 30, 2015, respectively. There were no amounts outstanding under the Revolving Credit Facility as of June 30, 2015.

Quarterly, principal payments are due under the Term Loan, which amortizes such that 10% of the outstanding principal is due during the first four years and the remaining 60% is due in the fifth year, including any remaining principal balance and any outstanding revolver balance at such time. The principal amount of unpaid maturities per the Amended Credit Agreement is as follows (in thousands):

2015, remainder thereof	$	—
2016	—
2017	—
2018	20,950
Total	$	20,950

The Company intends to continue making quarterly payments during 2015 and reclassified $4.0 million as current on the accompanying Condensed Consolidated Balance Sheet as of June 30, 2015.

4.00% Convertible Senior Notes

On June 25, 2012, the Company issued $105.0 million principal amount of 4.00% Convertible Senior Notes ("4.00% Convertible Notes") due July 1, 2019. The net proceeds, after debt issuance costs totaling $3.9 million from the 4.00% Convertible Notes offering, were $101.1 million. The 4.00% Convertible Notes bear interest of 4.00% per year payable semi-annually in arrears on January 1 and July 1 of each year, beginning on January 1, 2013 until the maturity date of July 1, 2019, unless converted, redeemed or repurchased earlier. The debt issuance costs are being amortized over the effective life of the 4.00% Convertible Notes, which is seven years.

Holders of the 4.00% Convertible Notes may convert their 4.00% Convertible Notes into shares of the Company’s stock at their option any time prior to the close of business on the business day immediately preceding the maturity date. The 4.00% Convertible Notes are initially convertible into approximately 170.0319 shares of the Company’s common stock per $1,000 principal amount of notes, which equates to 17,857,143 shares of common stock, or an initial conversion price of $5.88 per share of common stock. The conversion rate is subject to certain customary anti-dilution adjustments. In addition, following certain corporate events that occur prior to the maturity date, the Company will increase the conversion rate for a holder who elects to convert its notes in connection with such a corporate event in certain circumstances. Holders may also require the Company to repurchase for cash their notes upon certain fundamental changes.

On or after July 1, 2017, the Company can redeem for cash all or part of the 4.00% Convertible Notes if the last reported sale price per share of the Company’s common stock has been at least 130% of the conversion price then in effect for at least 20 trading days during any 30 consecutive trading day period ending within 5 trading days prior to the date on which the Company provides notice of redemption. The redemption price will be equal to 100% of the principal amount of the 4.00% Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. If the Company calls the 4.00% Notes for redemption, a holder of notes may convert its notes only until the close of business on the scheduled trading day immediately preceding the redemption date unless the Company fails to pay the redemption price (in which case a holder of notes may convert such notes until the redemption price has been paid or duly provided for).

As of June 30, 2015, the outstanding balance on the 4.00% Convertible Notes was $105.0 million and interest incurred for the three and six months ended June 30, 2015 was $1.2 million and $2.4 million, respectively.

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LEGAL PROCEEDINGS

6 Months Ended

Jun. 30, 2015

Commitments and Contingencies Disclosure [Abstract]

LEGAL PROCEEDINGS

LEGAL PROCEEDINGS

The Company has been in the past, and continues to be, a party to litigation, which has consumed, and may continue to consume, substantial financial and managerial resources. The Company could incur substantial costs and divert the attention of management and technical personnel in defending against litigation, and any adverse ruling or perception of an adverse ruling could have a material adverse impact on the Company’s stock price. In addition, any adverse ruling could have a material adverse impact on the Company’s cash flows and financial condition. The results of any litigation or any other legal proceedings are uncertain and, as of the date of this report, the Company has not accrued any liability with respect to any of the litigation matters listed below:

Enzo Litigation

Southern District of New York Case: On October 28, 2003, Enzo Life Sciences, Inc., a wholly-owned subsidiary of Enzo Biochem, Inc. (collectively "Enzo"), filed a complaint against the Company that is pending in the United States District Court for the Southern District of New York for breach of contract, injunctive relief and declaratory judgment. The Enzo complaint relates to a 1998 distributorship agreement with Enzo under which the Company served as a non-exclusive distributor of certain reagent labeling kits supplied by Enzo. On November 10, 2003, the Company filed a complaint against Enzo in the United States District Court for the Southern District of New York for declaratory judgment, breach of contract and injunctive relief relating to the 1998 agreement. On April 22, 2014, the Company entered into a settlement agreement with Enzo with respect to these two lawsuits. Pursuant to the agreement the Company agreed to pay Enzo $5.1 million and recorded the litigation settlement charge within the results of operations in the first three months of 2014. The settlement agreement does not include the Delaware Case described below.

Delaware Case: On April 6, 2012, Enzo filed a complaint against the Company in the United States District Court for the District of Delaware. In the complaint, plaintiff alleges that Affymetrix is infringing U.S. Patent No. 7,064,197 by making and selling certain GeneChip® products. The plaintiff seeks a preliminary and permanent injunction enjoining the Company from further infringement and unspecified monetary damages. The Company will vigorously defend against the plaintiff’s case. No trial date is set for this action.

Administrative Proceedings

The Company’s intellectual property is subject to a number of significant administrative actions. These proceedings could result in the Company’s patent protection being significantly modified or reduced, and the incurrence of significant costs and the consumption of substantial managerial resources. For the thee and six months ended June 30, 2015 and 2014, the Company did not incur significant costs in connection with administrative proceedings.

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FAIR VALUE MEASUREMENTS (Details) - USD ($)	6 Months Ended	12 Months Ended
	Jun. 30, 2015	Dec. 31, 2014
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Other-than-temporary impairment charges	$ 0	$ 100,000
4.00% Convertible Senior Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	4.00%
Convertible debt fair value	$ 209,900,000

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NET INCOME (LOSS) PER COMMON SHARE (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Net income (loss)	$ 7,006	$ (911)	$ 11,392	$ (11,385)
Interest on convertible notes	1,191		2,381
Adjusted net income (loss)	$ 8,197	$ (911)	$ 13,773	$ (11,385)
Shares used in computing basic net income (loss) per common share	78,476	72,944	76,951	72,722
Employee stock options	1,559		1,604
Employee stock purchase plan	4		3
Restricted stock and restricted stock units	1,566		1,604
Convertible notes	17,857		17,857
Shares used in computing diluted net income (loss) per common share (in shares)	99,462	72,944	98,019	72,722
Basic net income (loss) per common share (in usd per share)	$ 0.09	$ (0.01)	$ 0.15	$ (0.16)
Diluted net income (loss) per common share (in usd per share)	$ 0.08	$ (0.01)	$ 0.14	$ (0.16)

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ACQUISITION (Tables)

6 Months Ended

Jun. 30, 2015

Business Combinations [Abstract]

Business Acquisition, Pro Forma Information

The following unaudited pro forma financial information presents the combined results of operations for the three and six months ended June 30, 2015 and 2014 as if the Acquisition had been completed on January 1, 2014, with adjustments to give effect to pro forma events that are directly attributable to the Acquisition. The unaudited pro forma results do not reflect any operating efficiencies or potential cost savings that may result from the consolidation of the operations of the Company and Eureka. Accordingly, these unaudited pro forma results are presented for informational purposes only and are not necessarily indicative of what the actual results of operations of the combined company would have been if the Acquisition had occurred at the beginning of the period presented, nor are they indicative of future results of operations (in thousands, except per share data):

	Three Months Ended   June 30,					Six Months Ended   June 30,
	2015		2014			2015		2014
Revenues	$	89,064	$	85,464		$	178,069	$	168,454
Net income (loss)	6,335		(1,346		)	10,676		(12,570		)
Basic earnings per share	0.08		(0.02		)	0.14		(0.17		)
Diluted earnings per share	0.08		(0.02		)	0.13		(0.17		)

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WARRANTIES (Tables)

6 Months Ended

Jun. 30, 2015

Product Warranties Disclosures [Abstract]

Changes in entity's product warranty liability

Changes to the Company’s product warranty liability for the six months ended June 30, 2015 are as follows (in thousands):

Balance at December 31, 2014	$	912
Additions charged to cost of product sales	1,007
Repairs and replacements	(841		)
Balance at June 30, 2015	$	1,078

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LONG-TERM DEBT OBLIGATIONS, TERM LOAN MATURITIES (Details) - Secured Debt [Member] $ in Thousands	Jun. 30, 2015 USD ($)
Debt Instrument [Line Items]
2015, remainder thereof	$ 0
2016	0
2017	0
2018	20,950
Total debt	$ 20,950

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STOCKHOLDERS' EQUITY AND SHARE-BASED COMPENSATION EXPENSE SHARE-BASED COMPENSATION PLANS NARRATIVE (Details) - Jun. 30, 2015 - USD ($) shares in Millions, $ in Millions	Total
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Common stock reserved for future issuance (in shares)	6.6
Unrecognized share-based compensation expense	$ 17.5
Weighted-average term of unrecognized share-based compensation expense, stock options	2 years 1 month 17 days
Weighted-average term of unrecognized share-based compensation expense, restricted stock	1 year 10 months 7 days

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CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Statement of Comprehensive Income [Abstract]
Unrealized change in available-for-sale and non-marketable securities, Tax	$ 0	$ (545)	$ 0	$ 256
Unrealized change in cash flow hedges, Tax	$ 0	$ 0	$ 0	$ 0

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DERIVATIVE FINANCIAL INSTRUMENTS

6 Months Ended

Jun. 30, 2015

Derivative Instruments and Hedging Activities Disclosure [Abstract]

DERIVATIVE FINANCIAL INSTRUMENTS

DERIVATIVE FINANCIAL INSTRUMENTS

The Company derives a portion of its revenues in foreign currencies, predominantly in Europe and Japan, as part of its ongoing business operations. In addition, a portion of its assets are held in the foreign currencies of its subsidiaries. The Company enters into foreign currency forward contracts to manage a portion of the volatility related to transactions that are denominated in foreign currencies. The Company’s foreign currency forward contracts are entered into for periods consistent with the related underlying exposures and do not constitute positions that are independent of those exposures.

The Company is exposed to the risk that the counterparties to its hedges may be unable to meet the terms of these agreements. To mitigate the risk, only contracts with carefully selected highly-rated major financial institutions are entered into. In the event of non-performance by these counterparties, the asset position carrying values of the financial instruments represent the maximum amount of loss that can be incurred; however, no losses as a result of counterparty defaults are expected. The Company does not require and is not required to pledge collateral for these financial instruments. The Company does not enter into foreign currency forward contracts for trading or speculative purposes and is not party to any leveraged derivative instruments.

As of June 30, 2015 and December 31, 2014, the total notional values of the Company’s derivative assets and liabilities were as follows (in thousands):

	June 30, 2015		December 31, 2014
Euro	$	28,636	$	15,982
Japanese Yen	4,960		3,391
British Pound	6,087		1,784
Total	$	39,683	$	21,157

The Company records all derivative assets and liabilities on the accompanying Condensed Consolidated Balance sheets at fair value. The following table shows the Company’s derivatives as of June 30, 2015 and December 31, 2014 (in thousands):

	June 30, 2015		December 31, 2014		Balance Sheet Classification
Derivative assets:
Foreign exchange contracts	$	1,111	$	1,258	Prepaid expenses and other current assets
Derivative liabilities:
Foreign exchange contracts	433		—		Accounts payable and accrued liabilities

The effective portions of designated cash flow hedges are recorded in OCI until the hedged item is recognized in operations. Derivatives that are not designated as hedging instruments and the ineffective portions of cash flow hedges are adjusted to fair value through operations.

Derivative instruments designated as cash flow hedges must be de-designated as hedges when it is probable the forecasted hedged transaction will not occur in the initially identified time period or within a subsequent two-month time period. Deferred gains and losses associated with such derivative instruments are reclassified immediately into operations through Other income (expense), net on the Condensed Consolidated Statements of Operations. Any subsequent changes in fair value of such derivative instruments are reflected in Other income (expense), net unless they are re-designated as hedges of other transactions.

All derivative assets and liabilities were designated as hedging relationships as of June 30, 2015 and December 31, 2014.

The following table shows the effect, net of tax, of the Company’s derivative instruments on the accompanying Condensed Consolidated Statements of Operations and OCI for the three and sixmonths endedJune 30, 2015and 2014 (in thousands):

	Three Months Ended   June 30,						Six Months Ended   June 30,
	2015			2014			2015			2014
Derivatives in cash flow hedging relationships:
Net loss recognized in OCI	$	(2,403	)	$	(181	)	$	(615	)	$	(478	)
Net gain (loss) reclassified from accumulated OCI into Revenue	884			(314		)	2,669			(758		)
Net loss reclassified from accumulated OCI into Other income (expense), net	—			(7		)	—			(17		)
Net gain recognized in Other income (expense), net	49			19			62			1
Derivatives not designated as hedging relationships:
Net gain recognized in Other income (expense), net	—			11			—			12

As of June 30, 2015, the deferred amount recorded in OCI related to the Company's derivatives recorded is a net gain of $0.5 million and is expected to be recognized into earnings over the next 12 months.

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LONG-TERM DEBT OBLIGATIONS (Tables)

6 Months Ended

Jun. 30, 2015

Debt Disclosure [Abstract]

Schedule of Debt

The following table summarizes the carrying amount of the Company's borrowings (in thousands):

	June 30, 2015		December 31, 2014
Term loan	$	20,950	$	22,950
Convertible notes	105,000		105,000
Total debt	125,950		127,950
Less: current portion of long-term debt	4,000		4,000
Total long-term debt	$	121,950	$	123,950

Schedule of Maturities of Long-term Debt

The principal amount of unpaid maturities per the Amended Credit Agreement is as follows (in thousands):

2015, remainder thereof	$	—
2016	—
2017	—
2018	20,950
Total	$	20,950

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DERIVATIVE FINANCIAL INSTRUMENTS ENTITY'S FOREIGN CURRENCY DERIVATIVES MEASURED AT FAIR VALUE (Details) - Foreign exchange contracts [Member] - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Prepaid expenses and other current assets [Member]
Derivative [Line Items]
Derivative assets:	$ 1,111	$ 1,258
Accounts payable and accrued liabilities [Member]
Derivative [Line Items]
Derivative liabilities:	$ 433	$ 0

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SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Tables)

6 Months Ended

Jun. 30, 2015

Accounting Policies [Abstract]

Components of accumulated other comprehensive income, net of tax

The following table summarizes the amounts reclassified out of accumulated other comprehensive loss, net of tax, for the six months ended June 30, 2015 (in thousands):

	December 31, 2014			(Decrease)/ Increase			Reclassification Adjustments			June 30, 2015
Foreign currency translation adjustment	$	(2,933	)	$	(6,612	)	$	—		$	(9,545	)
Unrealized change in non-marketable securities	1,219			261			—			1,480
Unrealized change in cash flow hedges	1,102			2,054			(2,669		)	487
Total accumulated other comprehensive loss, net of tax	$	(612	)	$	(4,297	)	$	(2,669	)	$	(7,578	)