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FORM 4UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
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Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).
1. Name and Address of Reporting Person*
RUNKEL JOHN F JR

(Last)(First)(Middle)
C/O AFFYMETRIX, INC., 3420 CENTRAL EXPRESSWAY

(Street)
SANTA CLARACA95051

(City)(State)(Zip)
2. Issuer Name and Ticker or Trading Symbol
AFFYMETRIX INC [AFFX]
5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
Director10% Owner
XOfficer (give title below)Other (specify below)
EVP and General Counsel
3. Date of Earliest Transaction (Month/Day/Year)
08/20/2009
4. If Amendment, Date of Original Filed (Month/Day/Year)
6. Individual or Joint/Group Filing (Check Applicable Line)
XForm filed by One Reporting Person
Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3)
2. Transaction Date (Month/Day/Year)2A. Deemed Execution Date, if any (Month/Day/Year)3. Transaction Code
(Instr. 8)
4. Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5)
5. Amount of Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 3 and 4)
6. Ownership Form: Direct (D) or Indirect (I)
(Instr. 4)
7. Nature of Indirect Beneficial Ownership
(Instr. 4)
CodeVAmount(A) or (D)Price
Common Stock 08/20/2009 A  8,000 (1) A$ 0 38,000 D  

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned
(e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security
(Instr. 3)
2. Conversion or Exercise Price of Derivative Security3. Transaction Date (Month/Day/Year)3A. Deemed Execution Date, if any (Month/Day/Year)4. Transaction Code
(Instr. 8)
5. Number of Derivative Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4, and 5)
6. Date Exercisable and Expiration Date
(Month/Day/Year)
7. Title and Amount of Underlying Securities
(Instr. 3 and 4)
8. Price of Derivative Security
(Instr. 5)
9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 4)
10. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 4)
11. Nature of Indirect Beneficial Ownership
(Instr. 4)
CodeV(A)(D)Date ExercisableExpiration DateTitleAmount or Number of Shares
Option to Purchase Common Stock $ 8.29 08/20/2009 A  35,000   (2)08/20/2016 Common Stock 35,000 $ 0 35,000 D  
Explanation of Responses:
1. Restricted stock award vests in equal annual installments over four years from the grant date.
2. Option becomes exercisable in equal annual installments over four years from the grant date.
/s/ John F. Runkel, Jr.08/21/2009
** Signature of Reporting PersonDate
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 4(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB Number.

                  POWER OF ATTORNEY

       Know all persons by these presents, that the 
undersigned hereby constitutes and appoints each of 
Sandra E. Wells, Vice President and Chief Intellectual 
Property Counsel, and Siang H. Chin, Vice President 
and Chief Corporate Counsel, as the undersigned's true 
and lawful attorney-in-fact to:
       (1)         execute for and on behalf of the 
undersigned, in the undersigned's capacity as a 
reporting person pursuant to Section 16 of the 
Securities Exchange Act of 1934, as amended (the 
"Exchange Act"), and the rules thereunder of 
Affymetrix, Inc. (the "Company"), Forms 3, 4 and 5 in 
accordance with Section 16(a) of the Exchange Act;
       (2)         do and perform any and all acts for 
and on behalf of the undersigned which may be 
necessary or desirable to complete and execute any 
such Form 3, 4 or 5 and timely file such form with the 
United States Securities and Exchange Commission and 
stock exchange or similar authority; and
       (3)         take any other action of any type 
whatsoever in connection with the foregoing which, in 
the opinion of any of such attorneys-in-fact, may be 
of benefit to, in the best interest of, or legally 
required by, the undersigned, it being understood that 
the documents executed by any of such attorneys-in-
fact on behalf of the undersigned pursuant to this 
Power of Attorney shall be in such form and shall 
contain such terms and conditions as any of such 
attorneys-in-fact may approve in the discretion of any 
of such attorneys-in-fact.

       The undersigned hereby grants to each such 
attorney-in-fact full power and authority to do and 
perform any and every act and thing whatsoever 
requisite, necessary, or proper to be done in the 
exercise of any of the rights and powers herein 
granted, as fully to all intents and purposes as the 
undersigned might or could do if personally present, 
with full power of substitution or revocation, hereby 
ratifying and confirming all that any of such 
attorneys-in-fact, or the substitute or substitutes of 
any of such attorneys-in-fact, shall lawfully do or 
cause to be done by virtue of this Power of Attorney 
and the rights and powers herein granted.  The 
undersigned acknowledges that the foregoing attorneys-
in-fact, in serving in such capacity at the request of 
the undersigned, are not assuming, nor is the Company 
assuming, any of the undersigned's responsibilities to 
comply with Section 16 of the Exchange Act.

       This Power of Attorney shall remain in full 
force and effect until the undersigned is no longer 
required to file Forms 3, 4 and 5 with respect to the 
undersigned's holdings of and transactions in 
securities issued by the Company, unless earlier 
revoked by the undersigned in a signed writing 
delivered to the foregoing attorneys-in-fact.

       IN WITNESS WHEREOF, the undersigned has caused 
this Power of Attorney to be executed as of this 20th 
day of October 2008.

Signature:   /s/ John F. (Rick) Runkel

Name:        John F. (Rick) Runkel

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