Affymetrix (AFFX)

Item 8.01 Other Events

On July 1, 2008, we were named as a defendant in a complaint filed by plaintiffs E8 Pharmaceuticals LLC and Massachusetts Institute of Technology (MIT) in the United States District Court of Massachusetts.  In the complaint, the plaintiffs allege that we are infringing one patent owned by MIT and licensed to E8 Pharmaceuticals by making and selling our GeneChip® products to customers and teaching our customers how to use the products.  The plaintiffs seek a permanent injunction enjoining us from further infringement, and unspecified monetary damages, including lost profits, enhanced damages pursuant to 35 U.S.C. § 284, costs, attorneys’ fees and other relief as the court deems just and proper.  We believe that the plaintiffs’ claims are without merit and will vigorously defend against the claims advanced in the complaint.

Forward Looking Statements

Except for historical information contained in this current report, the matters set forth in this current report, including statements related to the defense of the litigation described in this current report and any potential results of such litigation, are forward-looking statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995. These forward-looking statements are subject to risks and uncertainties that may cause actual results to differ materially, including the risks and uncertainties (i) that the litigation may result in significant costs and expenses and could divert management’s attention and resources, any of which could adversely affect our business, financial condition or results of operations, (ii) that we may not be successful in defending against these claims, (iii) that we could be forced to make a significant settlement or judgment payment to the plaintiffs and could be required to stop making and selling our GeneChip® products or obtain a license, and (iv) that if we were unable to obtain a license or design around the applicable patents, we would be unable to make or sell our GeneChip® products, which would have a material adverse affect on our business, financial condition, and results of operations, and other risks and uncertainties described from time to time in our filings with the Securities and Exchange Commission, including our annual report on Form 10-K for the year ended December 31, 2007 and subsequent filings. These forward-looking statements are based on current information that is likely to change and speak only as of the date hereof. You are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date of this current report. All forward-looking statements are qualified in their entirety by this cautionary statement, and we undertake no obligation to revise or update any forward-looking statement to reflect events or circumstances after the issuance of this current report.

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Item 8.01 Other Events

On January 30, 2008, Affymetrix, Inc. (the “Company”) completed the acquisition (the “Transaction”) of USB Corporation (“USB”), a company that develops, manufactures and markets an extensive line of molecular biology and biochemical reagent products.  The Transaction was completed pursuant to an Agreement and Plan of Merger (the “Merger Agreement”), dated December 15, 2007, between the Company, USB, the shareholders of USB, and Yew Acquisition, Inc., a wholly-owned subsidiary of the Company.  The Transaction was previously announced by the Company in its Current Report on Form 8-K dated December 15, 2007.

The purchase price for the Transaction was approximately $75,000,000 in cash.  A portion of the purchase price was placed in escrow and will be paid to the Company or USB shareholders based on USB’s revenues in 2008 and/or claims for indemnification during the escrow period.

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Item 8.01  Other Events

On November 13, 2007 Affymetrix issued a press release announcing its proposed offering of the Notes.  A copy of Affymetrix’ related press release is attached hereto as Exhibit 99.1.

On November 13, 2007, Affymetrix issued a press release announcing the pricing of its offering of the Notes.  A copy of Affymetrix’ related press release is attached hereto as Exhibit 99.2.

On November 16, 2007, Affymetrix issued a press release announcing the closing of its offering of the Notes.  A copy of Affymetrix’ related press release is attached hereto as Exhibit 99.3.

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NOTE 13—OTHER EVENTS

Default Under Convertible Notes

The Company violated the reporting covenant under the indentures governing the Company’s $120 million aggregate principal amount 0.75% Senior Convertible Notes due 2033 (the “Notes”) as a result of the Company’s failure to file its Form 10-Q for the quarter ended June 30, 2006 by the required deadline. As a consequence of these violations, the holders of the Notes had the right to accelerate the maturity of such Notes if they or the trustee provide the Company with notice of the default and the Company was unable to cure the default within 60 days after that notice.  The Company cured the default within 60 days of the notice by filing its Form 10-Q for the quarter ended June 30, 2006 on August 30, 2006.

NASDAQ Notice

On August 17, 2006, the Company announced that it requested a hearing before the NASDAQ Listing Qualifications Panel (the “Panel”) in response to the receipt of a NASDAQ Staff Determination letter dated August 17, 2006 indicating that the Company is not in compliance with the filing requirements for continued listing as set forth in Marketplace Rule 4310(c)(14). As anticipated, the letter was issued in accordance with NASDAQ procedures due to the delayed filing of the Company’s Form 10-Q for the quarter ended June 30, 2006. The Company returned to compliance by filing its Form 10-Q for the quarter ended June 30, 2006 on August 30, 2006 and therefore, a hearing before the Panel was not required.

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Item 8.01 Other Events.

     On August 30, 2006, a shareholder derivative lawsuit was filed in the United States District Court for the Northern District of California naming the Company as a nominal defendant and naming several of the Company's current and former officers and directors as defendants. The complaint alleges that the defendants breached their fiduciary duty by backdating stock option grants, as well as violations of federal securities laws in connection with the dissemination of the Company's financial and proxy statements, violations of Generally Accepted Accounting Principles and violations of Section 162(m) of the Internal Revenue Code. The complaint further alleges that the officer defendants were unjustly enriched as a result of their receipt and retention of backdated stock option grants. Plaintiff seeks to recover, on behalf of the Company, unspecified equitable relief and disgorgement of any backdated stock options or the proceeds of any related exercised stock options from the individual officer defendants, as well as an award of attorneys' fees and costs. The Company may be subject to other lawsuits from private plaintiffs concerning this subject area, and the Company does not currently expect to disclose these additional lawsuits which are based on allegations substantially similar to those described above. The Company expects to contest vigorously the backdating allegations in the complaint.

Gregory Schiffman, Executive Vice President and Chief Financial Officer, will be speaking at the Citigroup 2006 Healthcare Conference in Washington, DC on February 28, 2006. Mr. Schiffman’s remarks are expected to include the following matters:

We are establishing a probe array manufacturing facility in Singapore. This new facility will increase our manufacturing capacity, establish redundancy for array manufacturing and provide a source of array product for our international businesses. In February 2006, we successfully completed the first in a series of manufacturing tests to demonstrate the capability of the Singapore facility. Passing this milestone keeps us on track for Singapore commercial array production in the second half of 2006.

Recent production yields on the Mapping 500K Array Set consistently exceed 75% in our Sacramento facility. At current yields, we believe that we will have sufficient capacity to meet customer demand for the Mapping 500K Array Set in 2006.

More than 70 of our existing customers are currently scaling up production on the Mapping 500K Array Set and some of these customers are experiencing challenges in the scale up. Since many customers complete projects before reordering, this may affect the timing of the 500K product reorders. In addition, we believe that the market for whole genome mapping products has temporarily slowed as early technology adopters begin to report on their whole genome genotyping studies and customers evaluate claims of competitive products about future price and performance.

The factors described above may increase the risk around our expected revenue targets for the Mapping 500K Array Set.

All statements in this Current Report on Form 8-K 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 (including risks associated with the Company’s ability to achieve hoped for revenue targets for the Mapping 500K Array Set), higher gross margins, reduced operating expenses; uncertainties relating to technological approaches, manufacturing (including risks related to the Company’s ability to achieve hoped-for manufacturing yields for certain array products, including the ability to identify and resolve manufacturing problems and risks and uncertainties associated with establishing our new probe array manufacturing facility in Singapore), 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 for the year ended December 31, 2004 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.

The information furnished under Item 8.01 of this Current Report on Form 8-K, shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), nor shall it be deemed incorporated by reference into Affymetrix’ filings with the

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