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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)
In Thousands, unless otherwise specified
3 Months Ended
Mar. 31, 2015
Mar. 31, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:    
Net income (loss) $ 4,386us-gaap_NetIncomeLoss $ (10,474)us-gaap_NetIncomeLoss
Adjustments to reconcile net income (loss) to net cash provided by operating activities:    
Depreciation and amortization 5,515us-gaap_DepreciationDepletionAndAmortization 8,712us-gaap_DepreciationDepletionAndAmortization
Amortization of inventory step-up in fair value 0affx_CostOfGoodsSoldInventoryStep-UpAmortization 2,896affx_CostOfGoodsSoldInventoryStep-UpAmortization
Share-based compensation 4,063affx_Share-BasedCompensationIncludingAcquisition 3,145affx_Share-BasedCompensationIncludingAcquisition
Deferred tax, net (977)affx_ChangeInDeferredTaxAssets (284)affx_ChangeInDeferredTaxAssets
(Gain) loss on sales of securities (59)us-gaap_AvailableforsaleSecuritiesGrossRealizedGainLossExcludingOtherThanTemporaryImpairments 15us-gaap_AvailableforsaleSecuritiesGrossRealizedGainLossExcludingOtherThanTemporaryImpairments
Other non-cash transactions 291us-gaap_OtherNoncashExpense 134us-gaap_OtherNoncashExpense
Changes in operating assets and liabilities:    
Accounts receivable, net (2,035)us-gaap_IncreaseDecreaseInAccountsReceivable 130us-gaap_IncreaseDecreaseInAccountsReceivable
Inventories 145us-gaap_IncreaseDecreaseInInventories (2,456)us-gaap_IncreaseDecreaseInInventories
Prepaid expenses and other assets (916)us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets 2,191us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets
Accounts payable and accrued liabilities (9,533)us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities 3,205us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities
Deferred revenue (309)us-gaap_IncreaseDecreaseInDeferredRevenueAndCustomerAdvancesAndDeposits (2,527)us-gaap_IncreaseDecreaseInDeferredRevenueAndCustomerAdvancesAndDeposits
Other long-term liabilities 771us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities (82)us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities
Net cash provided by operating activities 1,342us-gaap_NetCashProvidedByUsedInOperatingActivities 4,605us-gaap_NetCashProvidedByUsedInOperatingActivities
CASH FLOWS FROM INVESTING ACTIVITIES:    
Proceeds on sale of fixed assets 0us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment 106us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment
Capital expenditures (2,297)us-gaap_PaymentsToAcquirePropertyPlantAndEquipment (1,111)us-gaap_PaymentsToAcquirePropertyPlantAndEquipment
Purchase of technology rights (41)us-gaap_PaymentsToAcquireIntangibleAssets 0us-gaap_PaymentsToAcquireIntangibleAssets
Net cash used in investing activities (2,338)us-gaap_NetCashProvidedByUsedInInvestingActivities (1,005)us-gaap_NetCashProvidedByUsedInInvestingActivities
CASH FLOWS FROM FINANCING ACTIVITIES:    
Issuance of common stock, net of issuance costs 26,658us-gaap_ProceedsFromIssuanceOfCommonStock 184us-gaap_ProceedsFromIssuanceOfCommonStock
Repayments of long-term debt (1,000)us-gaap_RepaymentsOfSecuredDebt (3,250)us-gaap_RepaymentsOfSecuredDebt
Net cash provided by (used in) financing activities 25,658us-gaap_NetCashProvidedByUsedInFinancingActivities (3,066)us-gaap_NetCashProvidedByUsedInFinancingActivities
Effect of exchange rate changes on cash and cash equivalents (576)us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents 44us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents
Net increase in cash and cash equivalents 24,086us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease 578us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease
Cash and cash equivalents at beginning of period 79,923us-gaap_CashAndCashEquivalentsAtCarryingValue 57,128us-gaap_CashAndCashEquivalentsAtCarryingValue
Cash and cash equivalents at end of period $ 104,009us-gaap_CashAndCashEquivalentsAtCarryingValue $ 57,706us-gaap_CashAndCashEquivalentsAtCarryingValue