Document:

ex10-39.htm

    
      EXHIBIT
10.39

         

        March
9, 2010

         

        Tim
Barabe

         

        Dear
Tim:

         

        It
is our pleasure to offer you the position of Chief Financial Officer and
Executive Vice President with Affymetrix at an annual salary of $380,000
(bi-monthly $15,833.33), reporting to Kevin King, Chief Executive
Officer.  Your nomination as a Section 16(b) officer for Affymetrix
will be subject to review and approval by our Board of Directors at their next
meeting in May 2010.

         

        You
will be eligible to participate in the Affymetrix Annual Bonus Program with an
award level targeted at 50% of annual base salary.  If you begin employment
with Affymetrix by March 15, 2010 you will be entitled to a full year bonus
under the 2010 plan.  The actual bonus amount is determined each year
by the Compensation Committee of the Board of Directors based on corporate
achievement — financial performance and corporate goals — and your individual
goal achievement.  Bonus awards are subject to applicable withholding
of taxes and 401(k) contributions (if enrolled).

         

        Additionally,
we will recommend to the Compensation Committee of the Board of Directors of
Affymetrix that you be granted two equity awards.  The first is a Stock
Option Grant of 90,000 shares of common stock of Affymetrix.  These
options will vest 25% per year over a four (4) year period beginning on the
grant date, and will be granted (and, therefore priced) when approved by the
Compensation Committee.  The second is a grant of 20,000 shares of
restricted shares of common stock of Affymetrix.  These shares are not
stock options, but rather fully paid for shares of restricted stock. These
shares will vest 25% per year over a four (4) year period beginning on the grant
date, provided that you continue to be an employee of Affymetrix on such
anniversary dates.  These restricted shares will be granted when
approved by the Compensation Committee.  The terms of these equity
awards will be governed in all respects by the terms of the applicable
Affymetrix equity incentive plans and the equity award agreements that will be
provided to you after commencement of your employment.

         

        This
position is contingent on you relocating to the Bay Area. As part of this offer,
you will have up to June 30, 2011 to complete your relocation.

         

        We
will support your relocation with the following relocation benefits (total
amount of relocation benefits not to exceed $200,000) as managed by our
relocation partner, NRI:

         

        
          	
                  1.  

                	
                  We
      will pay the reasonable cost of moving your household goods, including
      shipment of 2 automobiles as well as a 1700 bottle personal wine
      collection, from your current residence to the Bay Area, provided that all
      of these items are moved to the Bay Area prior to June 30,
      2011.  We will also pay the reasonable cost of storing your
      household goods in the Bay Area until such time as you have either moved
      into your Bay Area residence or June 30, 2011, whichever is
      earlier.  In order for moving or storage costs to be considered
      “reasonable” they must be approved in advance through our relocation
      partner, NRI.

                

        

        
          	
                  2.  

                	
                  We
      will reimburse you for 180-days of temporary housing costs in the Bay Area
      that are incurred prior to June 30,
2011.

                

        

        
          	
                  3.  

                	
                  We
      will reimburse you for the cost of storage of household goods until June
      30, 2011, as approved through our partner,
NRI.

                

        

        
          	
                  4.  

                	
                  We
      will reimburse you for the actual cost of renting a car in the Bay Area
      for a period of no more than 90-days, provided that those expenses are
      incurred prior to June 30, 2011 and before your cars have been moved to
      the Bay Area.

                

        

        
          	
                  5.  

                	
                  We
      will reimburse you for the cost of one-way, coach class airfare for you
      and your family to relocate to the Bay Area or alternatively for expenses
      incurred while driving your family across country, whichever is
      less.

                

        

        
          	
                  6.  

                	
                  We
      will reimburse you for the actual cost of the real estate commission on
      the sale of your current address in Washington, D.C. metro area, costs not
      to exceed $150,000 (grossed-up.)

                

        

        
          	
                  7.  

                	
                  We
      will reimburse you for the cost of two four-day house hunting trips to the
      Bay Area for you and your spouse to give you an overview of Bay Area
      communities and a guided real estate tour in your choice of
      communities.  If these trips occur after you begin working for
      Affymetrix, we will only reimburse you for roundtrip airfare for your
      spouse.

                

        

         

        If
you voluntarily terminate your employment with Affymetrix (or Affymetrix
terminates your employment “for cause”) within twelve (12) months of the your
date of hire, your signature at the bottom of the last page of this letter
signifies your agreement to reimburse Affymetrix in full for the above
relocation expenses, with the exception of the expenses for temporary housing,
car rental, air travel and house hunting, incurred on your behalf.  If
you voluntarily terminate your employment with Affymetrix (or Affymetrix
terminates your employment “for cause”) within two (2) years of your date of
hire, you agree to reimburse Affymetrix for 50% of the above relocation
expenses.

         

        As
an additional condition of employment, we will require that you sign a copy of
the company's Confidentiality and Nondisclosure Agreement.

         

        Federal
Immigration Law requires that all employers verify each individual’s eligibility
to work in the United States, including U.S. citizens.  Your
employment offer is contingent upon your providing satisfactory proof of
identity and authorization to work in the United States.  Please bring
the appropriate original documentation on your first day of work.  A
list of acceptable I-9 documentation is attached for your review.

         

        Your
employment is at will and may be terminated by you or by Affymetrix for any or
no reason, with or without cause or notice.

         

        This
offer is contingent upon satisfactory completion of reference checks and
background checks.

         

        If
you have any questions, please feel free to contact me at (408)
731-5622.  To
indicate acceptance of this offer please return a signed copy of this letter to
me by the 3rd business day from the date of this offer, close of
business.  You may fax the letter back to me at (408)
731-5855.

         

        Sincerely,

         

        /s/
Lori Ciano

         

        Lori
Ciano

        Senior
Vice President, Human Resources

         

         

         

        Offer
Acceptance:

         

        /s/
Timothy
Barabe                                                                                3/11/10           
                                

        Tim
Barabe                                                                                             
Date

         

        March
15,
2010                                                         

        Start
Dateex10-40.htm

    
      EXHIBIT 10.40

       

      March 17,
2010

       

      John
Batty

       

      Re:           Separation
Agreement

       

      Dear
John:

       

      This
letter, upon your signature, will constitute the Separation Agreement (this
“Agreement”) between you and Affymetrix, Inc. (“Affymetrix”), on the terms of
your separation from employment with Affymetrix.

       

      1. Termination
Date.  This is to inform you that your employment is
terminated, effective March 15, 2010 (hereinafter “Termination
Date”).

       

      2. Final salary and vacation pay;
COBRA.  Regardless of whether you accept this Agreement, you
will be paid on or before your Termination Date the balance of your earned
salary and accrued vacation pay.  You will also receive payment of
your 2009 Corporate Bonus in the amount of $125,000 (one hundred and twenty-five
thousand dollars.)  As of your Termination Date, you will no longer be
eligible to participate in any of Affymetrix’s benefit or compensation plans,
except as provided by law or the terms of the applicable
plans.  Information regarding your rights to continuation of your
health insurance coverage under the terms of COBRA will be sent to you under
separate cover.  To the extent that you have such rights, nothing in
this Agreement will impair them.

       

      3. Status as of Termination Date; return
of company property; payment of amounts owed on corporate credit card;
reimbursement of expenses.  As of your Termination Date, you
will no longer represent to anyone that you are still an employee of Affymetrix
and will not say or do anything purporting to bind Affymetrix or any of its
affiliates.  As of your Termination Date, you will return to
Affymetrix any building key, security pass, or other access or identification
cards (including any business cards) and any company property that is currently
in your possession, including any documents, credit cards, computer equipment
and mobile phones.  By no later than ten days after your Termination
Date, you will clear all expense accounts and pay all amounts owed on any
corporate credit card(s) that Affymetrix previously issued to
you.  Affymetrix will reimburse you in accordance with its existing
policies for any legitimate expenses you incurred on company business prior to
the effective date of your termination.

       

      4. Severance
benefits.  Although you are not otherwise entitled to them, in
consideration of your acceptance of this Agreement, Affymetrix will provide to
you the following severance benefits:

       

      
        	
                a.  

              	
                Payable
      ten business days after the effective date of this agreement, twelve (12)
      months base pay less customary payroll deductions;
  and

              

      

       
 

      
        	
                b.  

              	
                Payable
      ten business days after the effective date of this agreement, payment of
      your Cobra premium for the first twelve (12) months  if you
      elect Cobra and are eligible for
coverage;

              

      

       
 

      
        	
                c.  

              	
                Six
      (6) months of outplacement services, commencing after the effective date
      of this Agreement. 

              

      

       

      5.      Release
of claims.

       

      a. On behalf
of yourself and your representatives, agents, heirs and assigns, you waive,
release, discharge and promise never to assert any and all claims, liabilities
or obligations of every kind and nature, whether known or unknown, suspected or
unsuspected that you ever had, now have or might have as of the effective date
of this Agreement against Affymetrix, its predecessors, subsidiaries, related
entities, officers, directors, shareholders, owners, agents, attorneys,
employees, successors, or assigns.  These released claims include,
without limitation, any claims arising from or related to your employment with
Affymetrix and the termination of your employment with
Affymetrix.  The released claims also specifically include, without
limitation, any claims arising under any federal, state and local statutory or
common law, Title VII of the Civil Rights Act, the federal Age Discrimination in
Employment Act, the California Fair Employment and Housing Act, the Americans
With Disabilities Act, the Employee Retirement Income Security Act, the law of
contract and tort, the federal WARN Act and its California counterpart, the
California Constitution and the California Labor Code, and all claims for
compensation, bonuses, severance pay, sick pay, vacation pay, expenses, costs
and attorney’s fees.

       

      b. You also
waive and release and promise never to assert any such claims, even if you do
not now know or believe that you have such claims.  You therefore
waive your rights under section 1542 of the Civil Code of California, which
states:

       

      A general
release does not extend to claims which the creditor does not know or suspect to
exist in his or her favor at the time of executing the release, which if known
by him or her must have materially affected his or her settlement with the
debtor.

       

      /s/ John C.
Batty                                                               
                                                 3/18/2010            

      Employee
Signature                                                                                                           Date

      

               
      6.       Confidentiality
of company information.  You acknowledge that in connection
with your employment with Affymetrix you have received certain trade secrets,
and non-public, confidential and proprietary business, financial and other
information concerning Affymetrix, its customers, affiliates, and the
like.  You will maintain as confidential all such information,
including all business plans, financial statements, budgets, projections,
marketing information, customer lists, prospective customer information,
technology, know-how, and intellectual property, whether in written, oral or
other form.  You agree that the foregoing information is strictly
confidential, and will not disclose this information to any third parties or
make use of it in any way.

       

      In the event you executed the
Affymetrix Confidentiality and Invention Agreement during the course of your
employment, you agree that it remains in effect subsequent to your termination
and will execute a certificate to that effect.  In the event you did
not execute the Confidentiality Agreement, you will do so prior to your receipt
of the severance benefits described above.

       

      7.        Non-disparagement.  You
will not disparage Affymetrix, any of its affiliates, related entities or any
past or present officers, directors or employees of Affymetrix, and will not say
or do anything that damages or impairs in any way the business organization,
goodwill, or reputation of Affymetrix or any of its affiliates or related
entities.

       

      8.       Cooperation
with information requests by Affymetrix.  Upon request by
Affymetrix, you will cooperate to the extent necessary to protect the interests
of Affymetrix or any of its subsidiaries, affiliates, or other related entities,
including without limitation, in providing any information that you have about
Affymetrix’s business and its operations and/or in providing truthful testimony
as a witness or declarant in connection with any potential future litigation
which may arise as to which you have any relevant information.

       

      9.        Non-solicitation.  You
acknowledge the highly confidential nature of certain information regarding
Affymetrix’s customers, affiliates and employees.  Therefore, you will
not use any such confidential information to solicit, call upon, divert or take
away, or attempt to solicit, call upon, divert or take away, any customers,
affiliates or employees of Affymetrix.

       

      10.     Remedies
in event of breach.  In the event that you breach any of your
obligations under this Agreement or as otherwise imposed by law, Affymetrix will
be entitled to immediate return of any and all benefits paid to you under this
Agreement and to obtain injunctive relief and all other relief provided by law
or equity.  All other duties and obligations under this Agreement,
however, including your waivers and releases, will remain in full force and
effect.

       

      11.        Arbitration.  The
parties agree that any and all disputes arising out of this Agreement or the
matters herein released, including all disputes arising out of your employment
with Affymetrix, the termination of your employment, or any other related matter
will be resolved by final and binding arbitration under the Employment Dispute
Resolution Rules of the American Arbitration Association.  This
arbitration remedy will be exclusive.  To invoke the arbitration
remedy, the complaining party must give notice in writing to the other party and
to the American Arbitration Association of his or its intention to arbitrate
within the statute of limitations applicable to the controversy and must first
submit the matter to a non-binding mediation before a mediator agreed upon by
the parties.  The arbitrator will have the authority to grant the same
remedies that could be awarded by a court of competent
jurisdiction.  The arbitrator will issue findings of fact and
conclusions of law supporting the award.  Any arbitration will be held
in Santa Clara.

       

      12.      Integrated
agreement.  Except as set forth in this Agreement, there are no
representations, promises, agreements or understandings between you and
Affymetrix about or pertaining to the separation of your employment with
Affymetrix, or Affymetrix’s obligations to you with respect to your employment
or any other matter mentioned above.  This Separation Agreement
therefore supersedes any prior written or oral representations, promises,
agreements and understandings regarding any the subject matter of this
Agreement.

       

      13.      Governing
law.  This Agreement will in all respects be interpreted and
governed under the laws of the State of California.

       

      14.      Severability.  If
any provision of this Agreement is determined by an arbitrator or court of
competent jurisdiction to be invalid, unenforceable or void, such provision
shall be enforced to the extent permitted by law and the remainder of this
Agreement shall remain in full force and effect.

       

      15.      Consideration and acceptance of
Agreement; Effective Date of Agreement.  You have 21 days to
consider and accept the terms of this Agreement (although you may accept it at
any time within those 21 days). Once signed, please send the Agreement to the
attention of Beckie Barnier, HR Representative, at Affymetrix’s address shown on
this first page of this Agreement.  The date of your signature will
constitute the “effective date” of this Agreement.

       

      16.      Age
Discrimination Claims. You acknowledge that the release of claims under
the Age Discrimination in Employment Act (“ADEA”) is subject to special waiver
protection.  Therefore, in accordance with that section, you
specifically agree that you knowingly and voluntarily release and waive any
rights or claims of discrimination under the ADEA.  In particular, you
represent and acknowledge that you understand the
following:  (a)  you are not waiving rights or claims for
age discrimination under the ADEA that may arise after the date you sign this
Release; (b) you are waiving rights or claims for age discrimination under the
ADEA in exchange for the payments described herein; (c) you will be given an
opportunity to consider fully the terms of this Release for twenty-one (21)
days, although you are not required to wait twenty-one (21) days before signing
this Release; (d) you have been advised to consult with an attorney of your
choosing before signing this Release; (e) you understand you have seven (7)
days after you sign this Release in which to revoke this Release, which can be
done by sending a certified letter to that effect to Affymetrix.  The
portion of the Release that pertains to the release of claims under the ADEA
shall not become effective or enforceable until the 7-day revocation period has
expired.  All other provisions of this Release will become effective
upon the date of your signature below.

       

      17.      No
Further Claims.   As of the date of your signature below,
you believe that you have received all wages, salary, compensation bonuses, and
benefits owed to you by Affymetrix (other than the severance referenced
herein.)  As of the date of your signature below, you have no
employment-related claims against Affymetrix and have no intention of filing
such claims in the future.  You further acknowledge that you have not
assigned any claims arising out of your employment to any third
party.

       

      We wish
you every success in your future endeavors.

       

      Sincerely,

       

      /s/ Lori
Ciano

      

      Lori
Ciano

      SVP,
Human Resources

      Affymetrix,
Inc.

      

      

      

      By
signing this letter, I acknowledge that I have carefully reviewed and considered
this Separation Agreement; that I fully understand all of its terms; and that I
voluntarily agree to them.

      

      

      

      

      Date:  3/18/2010               
                                                     /s/ John C.
Batty                
                                                                           

                      
John Batty

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