Affymetrix Reports Third Quarter 2006 Results

Share Name	Share Symbol	Market	Type
Affymetrix, Inc.	NASDAQ:AFFX	NASDAQ	Common Stock

Affymetrix (NASDAQ:AFFX)
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Affymetrix, Inc., (Nasdaq:AFFX) today reported its operating results for the third quarter of 2006. On a GAAP basis the Company reported net loss of approximately $14.2 million or $0.21 per diluted share, including restructuring charges of $10.0 million or $0.15 per diluted share and stock-based compensation expense of $3.6 million or $0.05 per diluted share, in the third quarter of 2006, as compared to net income of $9.4 million or $0.14 per diluted share in the third quarter of 2005. On January 1, 2006, the Company adopted FAS 123R and is reporting employee stock-based compensation expense in its GAAP results. Excluding the impact of FAS 123R, the Company reported non-GAAP net loss of approximately $11.0 million or $0.16 per diluted share in the third quarter of 2006. Total revenue for the quarter was $84.7 million, of which $4.6 million was related to the sale of products to Perlegen Sciences, Inc., as compared to total revenue of $83.4 million in the third quarter of 2005, of which $2.2 million was related to the sale of products to Perlegen. Product and product related revenue was $74.1 million for the third quarter of 2006, compared to $79.5 million in the same period in 2005. Third quarter sales included GeneChip� consumable revenue of $59.8 million, consisting of array revenue of $37.4 million, reagent revenue of $10.1 million, genotyping services revenue of $7.7 million and $4.6 million of Perlegen revenue. Additionally, the Company reported instrument revenue of $8.6 million. Affymetrix shipped 33 GeneChip Systems in the quarter, increasing the cumulative systems shipped to approximately 1480. Royalties and other revenue were $6.0 million for the third quarter of 2006 compared to $1.7 million in the third quarter of 2005. Total operating costs and expenses were $101.6 million for the third quarter of 2006, including the $10.0 million in restructuring charges previously mentioned, compared to $75.1 million in the third quarter of 2005. Cost of product and product related revenue was $32.5 million in the third quarter of 2006 compared to $23.4 million in the same period of 2005. Product and product related gross margin was 56.2 percent in the third quarter of 2006 compared to 70.6 percent in the third quarter of 2005. The primary factor which impacted the year-over-year gross margin comparison was the price reduction on the Company�s two-chip 500K Mapping Array which was instituted in July ahead of the planned shipments of a single-array 500K in the fourth quarter of 2006. This impacted gross margin by approximately $6 million or 8 points. Research and development expenses were $21.6 million during the third quarter of 2006 compared to $19.8 million in the third quarter of 2005.�Excluding the impact of FAS 123R, on a non-GAAP basis research and development expenses were $20.7 million during the third quarter of 2006 compared to $19.8 million in the third quarter of 2005. Selling, general and administrative expenses were $35.9 million for the third quarter of 2006 compared to $30.4 million in third quarter of 2005. In the third quarter of 2006, the Company incurred approximately $2.5 million of selling, general and administrative expenses associated with increased legal costs as well as expenses associated with the Company�s internal stock option review. Excluding the impact of FAS 123R, on a non-GAAP basis selling, general and administrative expenses were $33.6 million for the third quarter of 2006 compared to $30.2 million in the third quarter of 2005. Recent Highlights DNA Analysis Affymetrix has been selected to analyze more than 9,000 samples in a large-scale whole-genome association project for the Framingham Heart Study. As part of the SNP Health Association Resource project, Affymetrix will collaborate with the National Heart Lung and Blood Institute and the National Center for Biotechnology Information of the National Institutes of Health to identify genetic variants associated with heart, lung, blood and sleep disorders. The Autism Consortium has selected the single Affymetrix GeneChip Human Mapping 500K Array for the world's most comprehensive study on the genes associated with autism. The Autism Gene Discovery Project will be conducted across 3,700 samples by scientific experts from the Autism Consortium and the Broad Institute of MIT and Harvard. Researchers from Boston University and Howard University will perform the first genome-wide scan of an African American cohort searching for genes associated with obesity, hypertension, diabetes and metabolic syndrome using the Affymetrix 500K Array Set. Researchers at the Translational Genomics Research Institute (TGen) have used the Affymetrix 500K Array to discover a gene associated with memory performance in humans. The team's findings may be used to develop new medicines for memory-based diseases such as Alzheimer's and Parkinson's. The study was published in the Oct. 20, 2006 issue of Science. The Foundation for the National Institutes of Health (FNIH) announced that six major studies of brain, skin, and kidney disorders have been selected as the first to undergo whole genome analysis by the Genetic Association Information Network (GAIN). GAIN is a unique public-private partnership involving the NIH, Pfizer, Affymetrix, FNIH, Perlegen Sciences, Abbott, and the Broad Institute. RNA Analysis NCI and NHGRI announced grant awards in the Cancer Genome Atlas Pilot Project. The $100 million Project will test the use of large-scale genome analysis technologies in lung, brain, and ovarian cancer research. Affymetrix technology will be used at two institutions involved in the project. The Broad Institute of MIT and Harvard will use Affymetrix chips to look at expression and copy number changes. Lawrence Berkeley National Laboratory will use the Affymetrix Exon Arrays to look at cancer transcription profiles. The MicroArray Quality Control (MAQC) study, a collaborative effort led by the FDA and published in the September 8, 2006 issue of Nature Biotechnology, demonstrated that at a high level, gene expression signatures generated by microarrays are repeatable, further advancing the field towards widespread use in clinical applications. Affymetrix technology outperformed all other platforms in four areas: Reproducibility, Robustness, Sensitivity, and Controls. Molecular Diagnostics The Company has completed setup of Affymetrix Clinical Services Lab (ACSL), including filing Clinical Laboratory Improvement Amendments (CLIA) applications. Located in West Sacramento, the�purpose of ACSL is to accelerate adoption of GeneChip assays to clinical practice. This�lab will perform clinical tests, clinical trials, and assist in the development of clinical assays to accelerate the transition of GeneChip technologies under CLIA-validated, reproducible, standardized assay development practices. Pharmaceutical Wyeth has extended its agreement with Affymetrix for three more years, continuing the relationship that began in 1994. Under the agreement, Wyeth will apply Affymetrix technology in numerous areas of the drug discovery and development process. Wyeth was one of the first pharmaceutical companies to apply genomics in clinical research. Translational Medicine Affymetrix and Partners HealthCare have entered into a three-year translational research collaboration to develop microarray-based diagnostics for complex diseases such as newborn hearing loss, autism and hypertrophic cardiomyopathy. Researchers at Harvard Medical School, Partners HealthCare and Harvard Medical School-Partners HealthCare Center for Genetics and Genomics will create and validate microarray tests in CLIA laboratories. Affymetrix has entered into a five-year collaboration with the Peter MacCallum Cancer Centre (Peter Mac) in Melbourne, Australia, to analyze genomic information across large sets of patient samples. Peter Mac researchers will use Affymetrix arrays for translational research projects, beginning with studies on ovarian cancer and carcinoma of unknown primaries. Affymetrix and Zhejiang California Nanosystem Institute at Zhejiang University have entered into a collaboration to develop clinical applications using GeneChip technology in the areas of cancer, newborn genetic diseases and infectious diseases. This is Affymetrix' first translational medicine collaboration in China. Licensing NimbleGen has obtained a non-exclusive, worldwide license to a number of Affymetrix patents covering the manufacture, use and sales of nucleic acid microarrays and related products and services in the research field. Affymetrix' management team will host a conference call on October 25, 2006 at 2:00 p.m. PT to review its operating results for the third quarter of 2006. A live webcast can be accessed by visiting the Investor Relations section of the Company�s website at www.affymetrix.com. In addition, investors and other interested parties can listen by dialing domestic: (866) 500-AFFX, international: (706) 643-2771. A replay of this call will be available from 5:00 p.m. PT on October 25, 2006 until 8:00 p.m. PT on November 1, 2006 at the following numbers: domestic: (800) 642-1687, international: (706) 645-9291. The passcode for both replays is 8258660. An archived webcast of the conference call will be available under the Investor Relations section of the Company's website at www.affymetrix.com. About Affymetrix Affymetrix scientists invented the world's first high-density microarray in 1989 and began selling the first commercial microarray in 1994. Since then, Affymetrix GeneChip(R) technology has become the industry standard in molecular biology research. Affymetrix technology is used by the world's top pharmaceutical, diagnostic and biotechnology companies as well as leading academic, government and not-for-profit research institutes. More than 1,400 systems have been installed around the world and more than 7,000 peer-reviewed papers have been published using the technology. Affymetrix' patented photolithographic manufacturing process provides the most information capacity available today on an array, enabling researchers to use a whole-genome approach to analyzing the relationship between genetics and health. Affymetrix is headquartered in Santa Clara, Calif., with manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company maintains important sales and marketing operations in Europe and Asia and has about 1,100 employees worldwide. For more information about Affymetrix, please visit the company's website at www.affymetrix.com. Use of Non-GAAP Financial Measures In addition to disclosing financial results calculated in accordance with GAAP, the Company�s earnings release contains non-GAAP financial measures that exclude the effects of non-cash equity-based stock compensation expense as a result of the Company�s adoption of FAS 123R on January 1, 2006. The Company believes that the presentation of results excluding non-cash equity-based stock compensation expense provides meaningful supplemental information to both management and investors that is indicative of the Company�s core operating results. The Company used the Modified Prospective Method to adopt FAS 123R and did not restate prior year results for the impact of employee stock option expensing. Therefore, the Company believes these non-GAAP financial measures facilitate comparison of operating results across reporting periods. A reconciliation between the Company�s results of operations on a GAAP and non-GAAP basis for the periods reported is included as part of the condensed consolidated statements of operations at the end of the Company�s earnings release. The Company uses these non-GAAP financial measures when evaluating its financial results as well as for internal planning and forecasting purposes. The non-GAAP financial measures disclosed by the Company should not be considered a substitute for or superior to financial measures calculated in accordance with GAAP, and the financial results calculated in accordance with GAAP and reconciliations to those financial statements should be carefully evaluated. The non-GAAP financial measures used by the Company may be calculated differently from, and therefore may not be comparable to, similarly titled measures used by other companies. All statements in this press release that are not historical are "forward-looking statements"�under the federal securities laws. Such statements are subject to risks and uncertainties that could cause actual results to differ materially, including but not limited to: risks�related to�the Company's ability to achieve and sustain higher levels of revenue and improved�gross margins and operating income and reduced operating expenses (including risks related to the outcome of the Company's previously announced efforts to reduce expenses in the general and administrative functions including the rationalization of the Company's facilities); uncertainties relating to technological approaches, manufacturing (including risks related to resolving any manufacturing problems) and product development;�uncertainties relating to changes in senior management personnel�and structure; uncertainties related to cost and pricing of Affymetrix products;�risks relating to dependence on collaborative partners; uncertainties relating to sole source suppliers; uncertainties relating to FDA and other regulatory approvals; competition; risks relating to intellectual property of others and the uncertainties of patent protection; and risks relating to intellectual property and other litigation. These and other risk factors are discussed in Affymetrix' Form 10-K/A for the year ended December 31, 2005 and other SEC reports, including reports on Form 10-Q and Form 10-Q/A for subsequent periods. Affymetrix expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in Affymetrix' expectations or any change in events, conditions, or circumstances on which any such statements are based. PLEASE NOTE: Affymetrix, the Affymetrix logo and GeneChip are trademarks owned or used by Affymetrix, Inc. AFFYMETRIX,�INC. CONDENSED CONSOLIDATED BALANCE SHEETS (IN THOUSANDS) (UNAUDITED) � September 30,2006 December 31,2005 (Note 1) ASSETS Current assets: Cash and cash equivalents $ 66,487� $ 100,236� Available-for-sale securities � short-term 179,055� 184,696� Accounts receivable 65,097� 93,028� Accounts receivable from Perlegen Sciences 5,153� 4,082� Inventories 45,654� 35,980� Deferred tax assets�current portion 26,375� 26,230� Prepaid expenses and other current assets 7,584� 12,622� Total current assets 395,405� 456,874� Property and equipment, net 132,465� 85,560� Acquired technology rights, net 57,204� 61,426� Goodwill 124,787� 124,498� Deferred tax assets � long-term portion 18,087� 17,594� Notes receivable from employees 2,364� 1,824� Other assets 33,051� 27,318� $ 763,363� $ 775,094� � LIABILITIES AND STOCKHOLDERS� EQUITY Current liabilities: Accounts payable and accrued liabilities $ 60,939� $ 71,551� Deferred revenue � current portion 34,316� 35,644� Total current liabilities 95,255� 107,195� Deferred revenue � long-term portion 12,029� 15,606� Other long-term liabilities 5,279� 4,184� Convertible notes 120,000� 120,000� Stockholders� equity: Common stock 678� 672� Additional paid-in capital 660,732� 646,186� Deferred stock compensation �� (10,799) Accumulated other comprehensive loss (1,503) (1,227) Accumulated deficit (129,107) (106,723) Total stockholders� equity 530,800� 528,109� $ 763,363� $ 775,094� � Note�1: The condensed consolidated balance sheet at December�31, 2005 has been derived from the audited consolidated financial statements at that date included in the Company�s Form�10-K/A for the fiscal year ended December�31, 2005. AFFYMETRIX,�INC. CONDENSED CONSOLIDATED STATEMENTS OF (LOSS) INCOME (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS) (UNAUDITED) � Three Months Ended September 30, Nine Months Ended September 30, 2006� 2005� 2006� 2005� Revenue Product sales $ 56,139� $ 69,044� $ 183,154� $ 211,808� Product related revenue 17,971� 10,456� 45,621� 32,707� Total product and product related revenue 74,110� 79,500� 228,775� 244,515� Royalties and other revenue 5,969� 1,727� 10,263� 5,280� Revenue from Perlegen Sciences 4,593� 2,220� 12,091� 6,318� Total revenue 84,672� 83,447� 251,129� 256,113� � Costs and expenses: Cost of product sales 23,618� 20,755� 62,338� 57,986� Cost of product related revenue 8,859� 2,655� 22,712� 7,619� Cost of revenue from Perlegen Sciences 1,646� 1,359� 4,304� 4,351� Research and development 21,639� 19,835� 66,737� 57,724� Selling, general and administrative 35,865� 30,362� 114,107� 92,499� Stock-based compensation �� 141� �� 257� Restructuring 10,008� �� 10,008� �� Total costs and expenses 101,635� 75,107� 280,206� 220,436� (Loss) income from operations (16,963) 8,340� (29,077) 35,677� Interest income and other, net 2,942� 2,294� 10,949� 3,961� Interest expense (350) (413) (1,174) (1,129) � (Loss) income before income taxes (14,371) 10,221� (19,302) 38,509� Income tax benefit (provision) 216� (823) (3,082) (3,330) Net (loss) income $ (14,155) $ 9,398� $ (22,384) $ 35,179� � Basic net (loss) income per common share $ (0.21) $ 0.15� $ (0.33) $ 0.56� Diluted net (loss) income per common share $ (0.21) $ 0.14� $ (0.33) $ 0.52� � Shares used in computing basic net (loss) income per share 67,248� 63,786� 67,320� 63,112� Shares used in computing diluted net (loss) income per share 67,248� 70,463� 67,320� 69,966� AFFYMETRIX,�INC. RECONCILIATION OF GAAP TO NON-GAAP RESULTS OF OPERATIONS (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS) (UNAUDITED) � Three Months EndedSeptember 30, Nine Months EndedSeptember 30, 2006� 2005� 2006� 2005� GAAP net (loss) income $ (14,155) $ 9,398� $ (22,384) $ 35,179� Stock-based compensation: Cost of product sales(1) 408� �� 1,126� �� Research and development(1) 934� 7� 3,038� 10� Selling, general and administrative(1) 2,290� 134� 8,350� 247� Income tax effect(2) (509) (12) (3,124) (22) Non-GAAP net (loss) income $ (11,032) $ 9,527� $ (12,994) $ 35,414� � Non-GAAP diluted net (loss) income per share $ (0.16) � $ 0.14� $ (0.19) $ 0.52� � Shares used in computing non-GAAP diluted net (loss) income per share(3) 67,248� 70,463� 67,320� 69,966� Explanations for Non-GAAP adjustments included in table above: � (1) For the three and nine months ended September 30, 2006, the Company has added back stock-based compensation expense recorded under FAS 123R to compute its non-GAAP operating results. (2) Amount reflects the estimated tax impact on the above noted non-GAAP adjustments. (3) For the three and nine months ended September 30, 2006, the Company did not adjust the shares used in computing non-GAAP diluted net loss per share to conform to what the diluted shares would had been had it applied prior accounting standards as the Company was in a loss position. Affymetrix, Inc., (Nasdaq:AFFX) today reported its operating results for the third quarter of 2006. On a GAAP basis the Company reported net loss of approximately $14.2 million or $0.21 per diluted share, including restructuring charges of $10.0 million or $0.15 per diluted share and stock-based compensation expense of $3.6 million or $0.05 per diluted share, in the third quarter of 2006, as compared to net income of $9.4 million or $0.14 per diluted share in the third quarter of 2005. On January 1, 2006, the Company adopted FAS 123R and is reporting employee stock-based compensation expense in its GAAP results. Excluding the impact of FAS 123R, the Company reported non-GAAP net loss of approximately $11.0 million or $0.16 per diluted share in the third quarter of 2006. Total revenue for the quarter was $84.7 million, of which $4.6 million was related to the sale of products to Perlegen Sciences, Inc., as compared to total revenue of $83.4 million in the third quarter of 2005, of which $2.2 million was related to the sale of products to Perlegen. Product and product related revenue was $74.1 million for the third quarter of 2006, compared to $79.5 million in the same period in 2005. Third quarter sales included GeneChip(R) consumable revenue of $59.8 million, consisting of array revenue of $37.4 million, reagent revenue of $10.1 million, genotyping services revenue of $7.7 million and $4.6 million of Perlegen revenue. Additionally, the Company reported instrument revenue of $8.6 million. Affymetrix shipped 33 GeneChip Systems in the quarter, increasing the cumulative systems shipped to approximately 1480. Royalties and other revenue were $6.0 million for the third quarter of 2006 compared to $1.7 million in the third quarter of 2005. Total operating costs and expenses were $101.6 million for the third quarter of 2006, including the $10.0 million in restructuring charges previously mentioned, compared to $75.1 million in the third quarter of 2005. Cost of product and product related revenue was $32.5 million in the third quarter of 2006 compared to $23.4 million in the same period of 2005. Product and product related gross margin was 56.2 percent in the third quarter of 2006 compared to 70.6 percent in the third quarter of 2005. The primary factor which impacted the year-over-year gross margin comparison was the price reduction on the Company's two-chip 500K Mapping Array which was instituted in July ahead of the planned shipments of a single-array 500K in the fourth quarter of 2006. This impacted gross margin by approximately $6 million or 8 points. Research and development expenses were $21.6 million during the third quarter of 2006 compared to $19.8 million in the third quarter of 2005. Excluding the impact of FAS 123R, on a non-GAAP basis research and development expenses were $20.7 million during the third quarter of 2006 compared to $19.8 million in the third quarter of 2005. Selling, general and administrative expenses were $35.9 million for the third quarter of 2006 compared to $30.4 million in third quarter of 2005. In the third quarter of 2006, the Company incurred approximately $2.5 million of selling, general and administrative expenses associated with increased legal costs as well as expenses associated with the Company's internal stock option review. Excluding the impact of FAS 123R, on a non-GAAP basis selling, general and administrative expenses were $33.6 million for the third quarter of 2006 compared to $30.2 million in the third quarter of 2005. Recent Highlights DNA Analysis -- Affymetrix has been selected to analyze more than 9,000 samples in a large-scale whole-genome association project for the Framingham Heart Study. As part of the SNP Health Association Resource project, Affymetrix will collaborate with the National Heart Lung and Blood Institute and the National Center for Biotechnology Information of the National Institutes of Health to identify genetic variants associated with heart, lung, blood and sleep disorders. -- The Autism Consortium has selected the single Affymetrix GeneChip Human Mapping 500K Array for the world's most comprehensive study on the genes associated with autism. The Autism Gene Discovery Project will be conducted across 3,700 samples by scientific experts from the Autism Consortium and the Broad Institute of MIT and Harvard. -- Researchers from Boston University and Howard University will perform the first genome-wide scan of an African American cohort searching for genes associated with obesity, hypertension, diabetes and metabolic syndrome using the Affymetrix 500K Array Set. -- Researchers at the Translational Genomics Research Institute (TGen) have used the Affymetrix 500K Array to discover a gene associated with memory performance in humans. The team's findings may be used to develop new medicines for memory-based diseases such as Alzheimer's and Parkinson's. The study was published in the Oct. 20, 2006 issue of Science. -- The Foundation for the National Institutes of Health (FNIH) announced that six major studies of brain, skin, and kidney disorders have been selected as the first to undergo whole genome analysis by the Genetic Association Information Network (GAIN). GAIN is a unique public-private partnership involving the NIH, Pfizer, Affymetrix, FNIH, Perlegen Sciences, Abbott, and the Broad Institute. RNA Analysis -- NCI and NHGRI announced grant awards in the Cancer Genome Atlas Pilot Project. The $100 million Project will test the use of large-scale genome analysis technologies in lung, brain, and ovarian cancer research. Affymetrix technology will be used at two institutions involved in the project. The Broad Institute of MIT and Harvard will use Affymetrix chips to look at expression and copy number changes. Lawrence Berkeley National Laboratory will use the Affymetrix Exon Arrays to look at cancer transcription profiles. -- The MicroArray Quality Control (MAQC) study, a collaborative effort led by the FDA and published in the September 8, 2006 issue of Nature Biotechnology, demonstrated that at a high level, gene expression signatures generated by microarrays are repeatable, further advancing the field towards widespread use in clinical applications. Affymetrix technology outperformed all other platforms in four areas: Reproducibility, Robustness, Sensitivity, and Controls. Molecular Diagnostics -- The Company has completed setup of Affymetrix Clinical Services Lab (ACSL), including filing Clinical Laboratory Improvement Amendments (CLIA) applications. Located in West Sacramento, the purpose of ACSL is to accelerate adoption of GeneChip assays to clinical practice. This lab will perform clinical tests, clinical trials, and assist in the development of clinical assays to accelerate the transition of GeneChip technologies under CLIA-validated, reproducible, standardized assay development practices. Pharmaceutical -- Wyeth has extended its agreement with Affymetrix for three more years, continuing the relationship that began in 1994. Under the agreement, Wyeth will apply Affymetrix technology in numerous areas of the drug discovery and development process. Wyeth was one of the first pharmaceutical companies to apply genomics in clinical research. Translational Medicine -- Affymetrix and Partners HealthCare have entered into a three-year translational research collaboration to develop microarray-based diagnostics for complex diseases such as newborn hearing loss, autism and hypertrophic cardiomyopathy. Researchers at Harvard Medical School, Partners HealthCare and Harvard Medical School-Partners HealthCare Center for Genetics and Genomics will create and validate microarray tests in CLIA laboratories. -- Affymetrix has entered into a five-year collaboration with the Peter MacCallum Cancer Centre (Peter Mac) in Melbourne, Australia, to analyze genomic information across large sets of patient samples. Peter Mac researchers will use Affymetrix arrays for translational research projects, beginning with studies on ovarian cancer and carcinoma of unknown primaries. -- Affymetrix and Zhejiang California Nanosystem Institute at Zhejiang University have entered into a collaboration to develop clinical applications using GeneChip technology in the areas of cancer, newborn genetic diseases and infectious diseases. This is Affymetrix' first translational medicine collaboration in China. Licensing -- NimbleGen has obtained a non-exclusive, worldwide license to a number of Affymetrix patents covering the manufacture, use and sales of nucleic acid microarrays and related products and services in the research field. Affymetrix' management team will host a conference call on October 25, 2006 at 2:00 p.m. PT to review its operating results for the third quarter of 2006. A live webcast can be accessed by visiting the Investor Relations section of the Company's website at www.affymetrix.com. In addition, investors and other interested parties can listen by dialing domestic: (866) 500-AFFX, international: (706) 643-2771. A replay of this call will be available from 5:00 p.m. PT on October 25, 2006 until 8:00 p.m. PT on November 1, 2006 at the following numbers: domestic: (800) 642-1687, international: (706) 645-9291. The passcode for both replays is 8258660. An archived webcast of the conference call will be available under the Investor Relations section of the Company's website at www.affymetrix.com. About Affymetrix Affymetrix scientists invented the world's first high-density microarray in 1989 and began selling the first commercial microarray in 1994. Since then, Affymetrix GeneChip(R) technology has become the industry standard in molecular biology research. Affymetrix technology is used by the world's top pharmaceutical, diagnostic and biotechnology companies as well as leading academic, government and not-for-profit research institutes. More than 1,400 systems have been installed around the world and more than 7,000 peer-reviewed papers have been published using the technology. Affymetrix' patented photolithographic manufacturing process provides the most information capacity available today on an array, enabling researchers to use a whole-genome approach to analyzing the relationship between genetics and health. Affymetrix is headquartered in Santa Clara, Calif., with manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company maintains important sales and marketing operations in Europe and Asia and has about 1,100 employees worldwide. For more information about Affymetrix, please visit the company's website at www.affymetrix.com. Use of Non-GAAP Financial Measures In addition to disclosing financial results calculated in accordance with GAAP, the Company's earnings release contains non-GAAP financial measures that exclude the effects of non-cash equity-based stock compensation expense as a result of the Company's adoption of FAS 123R on January 1, 2006. The Company believes that the presentation of results excluding non-cash equity-based stock compensation expense provides meaningful supplemental information to both management and investors that is indicative of the Company's core operating results. The Company used the Modified Prospective Method to adopt FAS 123R and did not restate prior year results for the impact of employee stock option expensing. Therefore, the Company believes these non-GAAP financial measures facilitate comparison of operating results across reporting periods. A reconciliation between the Company's results of operations on a GAAP and non-GAAP basis for the periods reported is included as part of the condensed consolidated statements of operations at the end of the Company's earnings release. The Company uses these non-GAAP financial measures when evaluating its financial results as well as for internal planning and forecasting purposes. The non-GAAP financial measures disclosed by the Company should not be considered a substitute for or superior to financial measures calculated in accordance with GAAP, and the financial results calculated in accordance with GAAP and reconciliations to those financial statements should be carefully evaluated. The non-GAAP financial measures used by the Company may be calculated differently from, and therefore may not be comparable to, similarly titled measures used by other companies. All statements in this press release that are not historical are "forward-looking statements" under the federal securities laws. Such statements are subject to risks and uncertainties that could cause actual results to differ materially, including but not limited to: risks related to the Company's ability to achieve and sustain higher levels of revenue and improved gross margins and operating income and reduced operating expenses (including risks related to the outcome of the Company's previously announced efforts to reduce expenses in the general and administrative functions including the rationalization of the Company's facilities); uncertainties relating to technological approaches, manufacturing (including risks related to resolving any manufacturing problems) and product development; uncertainties relating to changes in senior management personnel and structure; uncertainties related to cost and pricing of Affymetrix products; risks relating to dependence on collaborative partners; uncertainties relating to sole source suppliers; uncertainties relating to FDA and other regulatory approvals; competition; risks relating to intellectual property of others and the uncertainties of patent protection; and risks relating to intellectual property and other litigation. These and other risk factors are discussed in Affymetrix' Form 10-K/A for the year ended December 31, 2005 and other SEC reports, including reports on Form 10-Q and Form 10-Q/A for subsequent periods. Affymetrix expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in Affymetrix' expectations or any change in events, conditions, or circumstances on which any such statements are based. PLEASE NOTE: Affymetrix, the Affymetrix logo and GeneChip are trademarks owned or used by Affymetrix, Inc. -0- *T AFFYMETRIX, INC. CONDENSED CONSOLIDATED BALANCE SHEETS (IN THOUSANDS) (UNAUDITED) September 30, December 31, 2006 2005 ------------- ------------ (Note 1) ASSETS Current assets: Cash and cash equivalents $ 66,487 $ 100,236 Available-for-sale securities - short- term 179,055 184,696 Accounts receivable 65,097 93,028 Accounts receivable from Perlegen Sciences 5,153 4,082 Inventories 45,654 35,980 Deferred tax assets--current portion 26,375 26,230 Prepaid expenses and other current assets 7,584 12,622 ------------- ------------ Total current assets 395,405 456,874 Property and equipment, net 132,465 85,560 Acquired technology rights, net 57,204 61,426 Goodwill 124,787 124,498 Deferred tax assets -- long-term portion 18,087 17,594 Notes receivable from employees 2,364 1,824 Other assets 33,051 27,318 ------------- ------------ $ 763,363 $ 775,094 ============= ============ LIABILITIES AND STOCKHOLDERS' EQUITY Current liabilities: Accounts payable and accrued liabilities $ 60,939 $ 71,551 Deferred revenue -- current portion 34,316 35,644 ------------- ------------ Total current liabilities 95,255 107,195 Deferred revenue -- long-term portion 12,029 15,606 Other long-term liabilities 5,279 4,184 Convertible notes 120,000 120,000 Stockholders' equity: Common stock 678 672 Additional paid-in capital 660,732 646,186 Deferred stock compensation -- (10,799) Accumulated other comprehensive loss (1,503) (1,227) Accumulated deficit (129,107) (106,723) ------------- ------------ Total stockholders' equity 530,800 528,109 ------------- ------------ $ 763,363 $ 775,094 ============= ============ ------------------------------------------- Note 1: The condensed consolidated balance sheet at December 31, 2005 has been derived from the audited consolidated financial statements at that date included in the Company's Form 10-K/A for the fiscal year ended December 31, 2005. *T -0- *T AFFYMETRIX, INC. CONDENSED CONSOLIDATED STATEMENTS OF (LOSS) INCOME (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS) (UNAUDITED) Three Months Ended Nine Months Ended September 30, September 30, ------------------ ------------------- 2006 2005 2006 2005 --------- -------- --------- --------- Revenue Product sales $ 56,139 $69,044 $183,154 $211,808 Product related revenue 17,971 10,456 45,621 32,707 --------- -------- --------- --------- Total product and product related revenue 74,110 79,500 228,775 244,515 Royalties and other revenue 5,969 1,727 10,263 5,280 Revenue from Perlegen Sciences 4,593 2,220 12,091 6,318 --------- -------- --------- --------- Total revenue 84,672 83,447 251,129 256,113 --------- -------- --------- --------- Costs and expenses: Cost of product sales 23,618 20,755 62,338 57,986 Cost of product related revenue 8,859 2,655 22,712 7,619 Cost of revenue from Perlegen Sciences 1,646 1,359 4,304 4,351 Research and development 21,639 19,835 66,737 57,724 Selling, general and administrative 35,865 30,362 114,107 92,499 Stock-based compensation -- 141 -- 257 Restructuring 10,008 -- 10,008 -- --------- -------- --------- --------- Total costs and expenses 101,635 75,107 280,206 220,436 --------- -------- --------- --------- (Loss) income from operations (16,963) 8,340 (29,077) 35,677 Interest income and other, net 2,942 2,294 10,949 3,961 Interest expense (350) (413) (1,174) (1,129) --------- -------- --------- --------- (Loss) income before income taxes (14,371) 10,221 (19,302) 38,509 Income tax benefit (provision) 216 (823) (3,082) (3,330) --------- -------- --------- --------- Net (loss) income $(14,155) $ 9,398 $(22,384) $ 35,179 ========= ======== ========= ========= Basic net (loss) income per common share $ (0.21) $ 0.15 $ (0.33) $ 0.56 ========= ======== ========= ========= Diluted net (loss) income per common share $ (0.21) $ 0.14 $ (0.33) $ 0.52 ========= ======== ========= ========= Shares used in computing basic net (loss) income per share 67,248 63,786 67,320 63,112 ========= ======== ========= ========= Shares used in computing diluted net (loss) income per share 67,248 70,463 67,320 69,966 ========= ======== ========= ========= *T -0- *T AFFYMETRIX, INC. RECONCILIATION OF GAAP TO NON-GAAP RESULTS OF OPERATIONS (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS) (UNAUDITED) Three Months Ended Nine Months Ended September 30, September 30, ------------------ ------------------ 2006 2005 2006 2005 ---------- ------- --------- -------- GAAP net (loss) income $ (14,155) $9,398 $(22,384) $35,179 Stock-based compensation: Cost of product sales(1) 408 -- 1,126 -- Research and development(1) 934 7 3,038 10 Selling, general and administrative(1) 2,290 134 8,350 247 Income tax effect(2) (509) (12) (3,124) (22) ---------- ------- --------- -------- Non-GAAP net (loss) income $ (11,032) $9,527 $(12,994) $35,414 ========== ======= ========= ======== Non-GAAP diluted net (loss) income per share $ (0.16) $ 0.14 $ (0.19) $ 0.52 ================== ========= ======== Shares used in computing non- GAAP diluted net (loss) income per share(3) 67,248 70,463 67,320 69,966 ========== ======= ========= ======== Explanations for Non-GAAP adjustments included in table above: (1) For the three and nine months ended September 30, 2006, the Company has added back stock-based compensation expense recorded under FAS 123R to compute its non-GAAP operating results. (2) Amount reflects the estimated tax impact on the above noted non- GAAP adjustments. (3) For the three and nine months ended September 30, 2006, the Company did not adjust the shares used in computing non-GAAP diluted net loss per share to conform to what the diluted shares would had been had it applied prior accounting standards as the Company was in a loss position. *T

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AFFX Affymetrix, Inc.