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CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)
In Thousands, unless otherwise specified
12 Months Ended
Dec. 31, 2014
Dec. 31, 2013
Dec. 31, 2012
CASH FLOWS FROM OPERATING ACTIVITIES:      
Net loss $ (3,834)us-gaap_NetIncomeLoss $ (16,327)us-gaap_NetIncomeLoss $ (10,696)us-gaap_NetIncomeLoss
Adjustments to reconcile net loss to net cash provided by operating activities:      
Depreciation and amortization 30,677us-gaap_DepreciationDepletionAndAmortization 38,988us-gaap_DepreciationDepletionAndAmortization 36,068us-gaap_DepreciationDepletionAndAmortization
Amortization of inventory step-up in fair value 4,666us-gaap_CostOfGoodsSoldAmortization 14,876us-gaap_CostOfGoodsSoldAmortization 9,444us-gaap_CostOfGoodsSoldAmortization
Excess tax benefits for share-based compensation 0us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities 60us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities 0us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities
Share-based compensation 12,411affx_Share-BasedCompensationIncludingAcquisition 7,727affx_Share-BasedCompensationIncludingAcquisition 17,207affx_Share-BasedCompensationIncludingAcquisition
Deferred tax assets (2,078)affx_ChangeInDeferredTaxAssets (167)affx_ChangeInDeferredTaxAssets (34,003)affx_ChangeInDeferredTaxAssets
Property and equipment, net—held for sale 0affx_LongLivedAssetsHeld-For-SaleFinalImpairmentCharges 0affx_LongLivedAssetsHeld-For-SaleFinalImpairmentCharges 3,491affx_LongLivedAssetsHeld-For-SaleFinalImpairmentCharges
Gain on sale of product line 0affx_GainLossonSaleofProductLine (9,295)affx_GainLossonSaleofProductLine 0affx_GainLossonSaleofProductLine
Gain on sales of securities (2,532)us-gaap_AvailableforsaleSecuritiesGrossRealizedGainLossExcludingOtherThanTemporaryImpairments 218us-gaap_AvailableforsaleSecuritiesGrossRealizedGainLossExcludingOtherThanTemporaryImpairments (184)us-gaap_AvailableforsaleSecuritiesGrossRealizedGainLossExcludingOtherThanTemporaryImpairments
Other non-cash transactions 1,132us-gaap_OtherNoncashExpense 5,205us-gaap_OtherNoncashExpense 1,532us-gaap_OtherNoncashExpense
Changes in operating assets and liabilities:      
Accounts receivable, net 2,824us-gaap_IncreaseDecreaseInAccountsReceivable 2,347us-gaap_IncreaseDecreaseInAccountsReceivable (514)us-gaap_IncreaseDecreaseInAccountsReceivable
Inventories 603us-gaap_IncreaseDecreaseInInventories 2,455us-gaap_IncreaseDecreaseInInventories 12us-gaap_IncreaseDecreaseInInventories
Prepaid expenses and other assets (460)us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets (9)us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets 6,338us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets
Accounts payable and accrued liabilities 8,750us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities (816)us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities (21,655)us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities
Deferred revenue (9,859)us-gaap_IncreaseDecreaseInDeferredRevenueAndCustomerAdvancesAndDeposits 9,596us-gaap_IncreaseDecreaseInDeferredRevenueAndCustomerAdvancesAndDeposits (2,023)us-gaap_IncreaseDecreaseInDeferredRevenueAndCustomerAdvancesAndDeposits
Other long-term liabilities 1,183us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities (1,274)us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities (1,286)us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities
Net cash provided by operating activities 43,483us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations 53,584us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations 3,731us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations
CASH FLOWS FROM INVESTING ACTIVITIES:      
Acquisition of businesses, net of cash acquired 0us-gaap_PaymentsToAcquireBusinessesNetOfCashAcquired 0us-gaap_PaymentsToAcquireBusinessesNetOfCashAcquired (307,796)us-gaap_PaymentsToAcquireBusinessesNetOfCashAcquired
Proceeds from sales of available-for-sale securities 0us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities 9,364us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities 52,063us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities
Proceeds from maturities of available-for-sale securities 0us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities 0us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities 1,138us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities
Proceeds from sale of property and equipment 130us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment 0us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment 5,509us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment
Proceeds from sale of product line 0affx_ProceedsFromSaleofProductLine 11,832affx_ProceedsFromSaleofProductLine 0affx_ProceedsFromSaleofProductLine
Capital expenditures (7,891)us-gaap_PaymentsToAcquirePropertyPlantAndEquipment (4,808)us-gaap_PaymentsToAcquirePropertyPlantAndEquipment (8,166)us-gaap_PaymentsToAcquirePropertyPlantAndEquipment
Capital distribution from non-marketable investments 3,133us-gaap_ProceedsFromEquityMethodInvestmentDividendsOrDistributionsReturnOfCapital 0us-gaap_ProceedsFromEquityMethodInvestmentDividendsOrDistributionsReturnOfCapital 681us-gaap_ProceedsFromEquityMethodInvestmentDividendsOrDistributionsReturnOfCapital
Purchase of technology rights (43)us-gaap_PaymentsToAcquireIntangibleAssets (736)us-gaap_PaymentsToAcquireIntangibleAssets (2,362)us-gaap_PaymentsToAcquireIntangibleAssets
Net cash provided by (used in) investing activities (4,671)us-gaap_NetCashProvidedByUsedInInvestingActivities 15,652us-gaap_NetCashProvidedByUsedInInvestingActivities (258,933)us-gaap_NetCashProvidedByUsedInInvestingActivities
CASH FLOWS FROM FINANCING ACTIVITIES:      
Issuance of common stock, net 1,207us-gaap_ProceedsFromIssuanceOfCommonStock 825us-gaap_ProceedsFromIssuanceOfCommonStock 276us-gaap_ProceedsFromIssuanceOfCommonStock
Proceeds from term loan and revolver 0us-gaap_ProceedsFromRepaymentsOfSecuredDebt 48,000us-gaap_ProceedsFromRepaymentsOfSecuredDebt 80,500us-gaap_ProceedsFromRepaymentsOfSecuredDebt
Payments of term loan (16,500)us-gaap_RepaymentsOfSecuredDebt (81,826)us-gaap_RepaymentsOfSecuredDebt (11,724)us-gaap_RepaymentsOfSecuredDebt
Debt issuance costs 0us-gaap_PaymentsOfDebtIssuanceCosts (1,080)us-gaap_PaymentsOfDebtIssuanceCosts 0us-gaap_PaymentsOfDebtIssuanceCosts
Proceeds from issuance of 4.00% convertible senior notes 0us-gaap_ProceedsFromConvertibleDebt 0us-gaap_ProceedsFromConvertibleDebt 101,062us-gaap_ProceedsFromConvertibleDebt
Repurchase of 3.50% senior convertible notes 0us-gaap_RepaymentsOfConvertibleDebt (3,855)us-gaap_RepaymentsOfConvertibleDebt (91,614)us-gaap_RepaymentsOfConvertibleDebt
Net cash (used in) provided by financing activities (15,293)us-gaap_NetCashProvidedByUsedInFinancingActivities (37,936)us-gaap_NetCashProvidedByUsedInFinancingActivities 78,500us-gaap_NetCashProvidedByUsedInFinancingActivities
Effect of exchange rate changes on cash and cash equivalents (724)us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents 157us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents 436us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents
Net increase (decrease) in cash and cash equivalents 22,795us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease 31,457us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease (176,266)us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease
Cash and cash equivalents at beginning of period 57,128us-gaap_CashAndCashEquivalentsAtCarryingValue 25,671us-gaap_CashAndCashEquivalentsAtCarryingValue 201,937us-gaap_CashAndCashEquivalentsAtCarryingValue
Cash and cash equivalents at end of period 79,923us-gaap_CashAndCashEquivalentsAtCarryingValue 57,128us-gaap_CashAndCashEquivalentsAtCarryingValue 25,671us-gaap_CashAndCashEquivalentsAtCarryingValue
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION:      
Cash paid for interest 5,434us-gaap_InterestPaid 12,456us-gaap_InterestPaid 6,968us-gaap_InterestPaid
Cash (paid) received for income taxes, net of refunds $ (1,563)us-gaap_IncomeTaxesPaidNet $ (2,222)us-gaap_IncomeTaxesPaidNet $ 3,905us-gaap_IncomeTaxesPaidNet