| 1. | I      have reviewed this report on Form 10-K for the year ended December      31, 2009 of Affymetrix, Inc.; |
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| 2. | Based      on my knowledge, this report does not contain any untrue statement of a      material fact or omit to state a material fact necessary to make the      statements made, in light of the circumstances under which such statements      were made, not misleading with respect to the period covered by this      report; |
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| 3. | Based      on my knowledge, the financial statements, and other financial information      included in this report, fairly present in all material respects the      financial condition, results of operations and cash flows of the      registrant as of, and for, the periods presented in this      report; |
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| 4. | The      registrant’s other certifying officer and I are responsible for      establishing and maintaining disclosure controls and procedures (as      defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and      internal control over financial reporting (as defined in Exchange Act      Rules 13a-15(f) and 15d-15(f)) for the registrant and      have: |
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|   | (a) | Designed such disclosure      controls and procedures, or caused such disclosure controls and procedures      to be designed under our supervision, to ensure that material information      relating to the registrant, including its consolidated subsidiaries, is      made known to us by others within those entities, particularly during the      period in which this report is beingprepared; |
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|   | (b) | Designed such internal      control over financial reporting, or caused such internal control over      financial reporting to be designed under our supervision, to provide      reasonable assurance regarding the reliability of financial reporting and      the preparation of financial statements for external purposes in      accordance with generally accepted accounting  principles; |
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|   | (c) | Evaluated the      effectiveness of the registrant’s disclosure controls and procedures and      presented in this report our conclusions about the effectiveness of the      disclosure controls and procedures, as of the end of the period covered by      this report, based on such evaluation;and |
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|   | (d) | Disclosed in this report      any change in the registrant’s internal control over financial reporting      that occurred during the registrant’s most recent fiscal quarter (the      registrant’s fourth fiscal quarter in the case of an annual report) that      has materially affected, or is reasonably likely to materially affect, the      registrant’s internal control over financial reporting;  and |
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| 5. | The      registrant’s other certifying officer(s) and I have disclosed, based      on our most recent evaluation of internal control over financial      reporting, to the registrant’s auditors and the audit committee of the      registrant’s board of directors (or persons performing the equivalent      functions): |
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|   | (a) | All significant      deficiencies and material weaknesses in the design or operation of      internal control over financial reporting which are reasonably likely to      adversely affect the registrant’s ability to record, process, summarize      and report financial information;and |
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|   | (b) | Any fraud, whether or not      material, that involves management or other employees who have a      significant role in the registrant’s internal control over financial      reporting. |
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| March      1, 2010 |        /s/ John C. Batty |
|--------------------|-------------------------------|
|               | Name:                         | John      C. Batty |
|               | Title:                        | Executive      Vice President and Chief FinancialOfficer |