Affymetrix Participates in Study to Advance MicroArray Technology Towards Widespread Clinical Use; GeneChip(R) Technology Demonstrates Top Performance in MicroArray Quality Control Study.

SANTA CLARA, Calif. -- Affymetrix Inc. (Nasdaq:AFFX) announced today the publication of the MicroArray Quality Control (MAQC) study, a collaborative effort led by the FDA that included 137 scientists from private and public sector laboratories. Affymetrix and other microarray and reagent manufacturers participated in the two-year initiative designed to address the reproducibility of data generated from microarrays.

The study, published in the Sept. 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.

"The MAQC study has demonstrated that by practicing good scientific method in the laboratory, researchers can obtain accurate, reproducible data from microarrays," said Janet Warrington, Ph.D., vice president, Emerging Markets and Molecular Diagnostics R&D at Affymetrix, who co-authored three of the eight manuscripts published as part of the study. "Microarrays are an important tool for advancing personalized medicine, drug target discovery, toxicogenomics and related fields, and this study supplies valuable performance information supporting the expansion of genomics in clinical applications."

In addition to advancing the field as a whole, the data obtained from the study showed that Affymetrix GeneChip(R) arrays demonstrated the best reproducibility within and across sites, an element critical for the success of clinical studies. Affymetrix GeneChip arrays also showed the best apparent power in detecting changes in gene expression, better enabling the discovery of novel biomarkers that are the objective of many disease-related studies.

"The MAQC study clearly shows why GeneChip technology is considered the gold standard in the microarray industry--Affymetrix provides the highest quality and value for microarray-based research," said Lianne McLean, senior director, Academic Product Marketing at Affymetrix. "We encourage the scientific community to read the manuscripts and to review the data. The results of the study speak for themselves."

Affymetrix outperformed other study participants in the following areas:

- Reproducibility - Affymetrix technology demonstrated the highest level of reproducibility and consistency within and across different test sites, an element critical for the success of any clinical study(1).

- Robustness - Affymetrix was shown to have the most robust platform--it was the only manufacturer that did not remove or repeat data from any sites(2).

- Sensitivity - Affymetrix technology demonstrated the best apparent power, or sensitivity, in detecting changes in gene expression(3).

- Controls - Affymetrix is the only participating platform that provides a comprehensive panel of controls, which is critical for the evaluation of clinical samples(4).

To generate the data for the study, six microarray manufacturers and the National Cancer Institute each selected three sites to run assays. At each site, 20 RNA samples were processed, for a total of 60 samples for each participant. The FDA analyzed the data using each vendor's recommended software, and compared the results.

Beginning Monday, the Affymetrix UserForum will feature continuing coverage of the MAQC study, including an interview with Dr. Warrington and a series of conference call symposia featuring other authors of the study. For more information and to register when available, please visit: http://www.affymetrix.com/userforum/index.uf.

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.

All statements in this press release that are not historical are "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix' "expectations," "beliefs," "hopes," "intentions," "strategies," or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected, including, but not limited to: risks of the Company's ability to achieve and sustain higher levels of revenue, higher gross margins, reduced operating expenses; uncertainties relating to technological approaches, manufacturing, product development; personnel retention; uncertainties related to cost and pricing of Affymetrix products; 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 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 its Quarterly Reports on Form 10-Q for subsequent quarterly 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 with regard thereto or any change in events, conditions or circumstances on which any such statements are based.

NOTE: Affymetrix, the Affymetrix logo, and GeneChip are registered trademarks owned or used by Affymetrix Inc.

(1) The MicroArray Quality Control (MAQC) Project shows interplatform reproducibility of gene expression measurements; Figure 1 and Figure 2.

(2) The MicroArray Quality Control (MAQC) Project shows interplatform reproducibility of gene expression measurements; Table 1. Supplementary Information on MAQC Study; Table S3.

(3) Supplementary Information on MAQC Study; Section H.

(4) Evaluation of external RNA controls for the assessment of microarray performance.