EXHIBIT 10.46

SECOND AMENDMENT TO CREDIT AGREEMENT
THIS SECOND AMENDMENT TO CREDIT AGREEMENT (this "Agreement") is entered into as
of December 5, 2012, by and among AFFYMETRIX, INC., a Delaware corporation (the
"Borrower"), the other Credit Parties signatory hereto, GENERAL ELECTRIC CAPITAL
CORPORATION, a Delaware corporation (in its individual capacity, "GE Capital"),
for itself and as agent for the Lenders (in such capacity, the "Agent"), and the
Lenders signatory hereto.  Unless otherwise specified herein, capitalized terms
used in this Agreement shall have the meanings ascribed to them in the Credit
Agreement (as hereinafter defined), as amended.
R E C I T A L S:
WHEREAS, Borrower, the other Credit Parties party thereto, the Agent and the
Lenders entered into that certain Credit Agreement, dated as of June 25, 2012
(as amended, restated, supplemented or otherwise modified prior to the date
hereof, the "Credit Agreement"); and
WHEREAS, the Credit Parties have requested that the Agent and the Lenders party
hereto amend certain provisions of the Credit Agreement, and the Agent and each
Lender party hereto agree to such amendments upon the terms and subject to the
conditions set forth herein.
NOW THEREFORE, in consideration of the premises and the mutual agreements set
forth, the receipt and sufficiency of which are hereby acknowledged, the parties
hereto hereby agree as follows:
1.  Amendment.  Section 6.1 of the Credit Agreement is hereby amended by
deleting  the  reference  to "$10,000,000"  set  forth  therein  and  replacing
 the  same  with "$10,000,000, or an amount up to $13,500,000 provided, that the
Capital Expenditure Limitation for the Fiscal Year ended December 31, 2013 shall
be decreased by the amount by which Capital Expenditures for the Fiscal Year
ended December 31, 2012 exceed $10,000,000".
2.  Conditions.  This Agreement shall be effective upon Agent's receipt of an
executed signature page to this Agreement from each Credit Party, the Agent and
the Required Lenders.
3.  Representations and Warranties of Credit Parties.  In order to induce the
Agent and the Required Lenders to enter into this Agreement, each Credit Party
represents and warrants to Agent and each Lender (which representations and
warranties shall survive the execution and delivery of this Agreement), that:
(a)  the execution, delivery and performance by each Credit Party of this
Agreement has been duly authorized by all necessary corporate action and this
Agreement is a legal, valid and binding obligation of such Credit Party
enforceable against such Credit Party in accordance  with  its  terms,  except
 as  such  enforceability  may  be  limited  by  applicable bankruptcy,
insolvency, reorganization, receivership, moratorium and similar Laws relating
to or affecting the enforceability of creditors' rights generally, and except
that the availability of equitable remedies is subject to the discretion of the
courts (regardless of whether enforcement is sought in a proceeding at law or in
equity);

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(b)  upon the effectiveness of this Agreement, all of the representations and
warranties contained in the Credit Agreement and in the other Loan Documents
(other than those which speak expressly only as of an earlier date) are true and
correct in all material respects on and as of the date of the effectiveness of
this Agreement after giving effect to this Agreement and the transactions
contemplated hereby;
(c)  neither the execution, delivery or performance of this Agreement by each
Credit Party nor the consummation of the transactions contemplated hereby or
thereby does or shall contravene, result in a breach of, or violate (i) any
provision of such Credit Party's certificate or articles of incorporation or
bylaws, or other organizational documents, (ii) any law or regulation, or any
order or decree of any court or government instrumentality, or (iii) any
indenture, mortgage, deed of trust, lease, agreement or other instrument to
which such Credit Party or any of its Subsidiaries is a party or by which such
Credit Party or any of its Subsidiaries or any of their property is bound,
except in any such case to the extent such conflict or breach has been waived by
a written waiver document, a copy of which has been delivered to Agent on or
before the date hereof or which could not reasonably be expected to have, either
individually or in the aggregate, a Material Adverse Effect; and
(d)  no Default or Event of Default exists or will result after giving effect to
this Agreement and the transactions contemplated hereby.
4.  Counterparts; Facsimile Signature.  This Agreement may be executed in any
number of counterparts and by different parties in separate counterparts, each
of which when so executed shall be deemed to be an original and all of which
taken together shall constitute one and the same agreement.  Signature pages may
be detached from multiple separate counterparts and attached to a single
counterpart.  Delivery of an executed signature page of this Agreement by
facsimile transmission or Electronic Transmission shall be as effective as
delivery of a manually executed counterpart hereof.
5.  Continuing Effect of the Credit Agreement.  Except as expressly set forth
herein, this Agreement shall not by implication or otherwise limit, impair,
constitute a waiver of, or otherwise affect the rights and remedies of the
Lenders or the Agent under the Credit Agreement and shall not alter, modify,
amend or in any way affect any of the terms, conditions, obligations, covenants
or agreements contained in the Credit Agreement, all of which are ratified and
affirmed in all respects and shall continue in full force and effect.  Nothing
herein shall be deemed to entitle the Credit Parties to a consent to, or a
waiver, amendment, modification or other change of, any of the terms,
conditions, obligations, covenants or agreements contained in the Credit
Agreement in similar or different circumstances.  This Agreement shall apply and
be effective only with respect to the provisions of the Credit Agreement
specifically referred to herein.  After the effectiveness of this Agreement, any
reference to the Credit Agreement shall mean the Credit Agreement as modified
hereby. This Agreement shall constitute a Loan Document.
6.  Governing Law.  THIS AGREEMENT SHALL BE GOVERNED BY AND CONSTRUED IN
ACCORDANCE WITH THE INTERNAL LAWS OF THE STATE OF NEW YORK.

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7.  Captions.  The captions and headings of this Agreement are for convenience
of reference only and shall not affect the interpretation of this Agreement.
8.  Reaffirmation.  The Credit Parties signatory hereto hereby reaffirm their
guaranties of the Obligations and reaffirm that the Obligations are and continue
to be secured by the security interest granted by the Credit Parties in favor of
the Agent under the Guaranty and Security Agreement and all of the terms,
conditions, provisions, agreements, requirements, promises, obligations, duties,
covenants and representations of the Credit Parties under such documents and
agreements entered into with respect to the obligations under the Credit
Agreement are incorporated herein by reference and are hereby ratified and
affirmed in all respects by the Credit Parties.  Each Credit Party acknowledges
that all references to "Credit Agreement" and "Obligations" in the Loan
Documents shall take into account the provisions of this Agreement and be a
reference to the "Credit Agreement" and the "Obligations" as amended hereby.
(signature pages follow)

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IN WITNESS WHEROF, the parties hereto have caused this Agreement to be duly
executed and delivered by the duly authorized officers as of the day and year
first above written.
AFFYMETRIX, INC.

By: /s/ Timothy Barabe

Name: Timothy Barabe

Title: EVP and CFO

USB CORPORATION

By: /s/ Timothy Barabe

Name: Timothy Barabe

Title: CFO

ANATRACE, INC.

By: /s/ David Roberts

Name: David Roberts

Title: CFO

EBIOSCIENCE HOLDING COMPANY, INC.

By: /s/ Timothy Barabe

Name: Timothy Barabe

Title: Vice President

EBIOSCIENCE, INC.

By: /s/ Timothy Barabe

Name: Timothy Barabe

Title: Vice President

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[Signature Page to Second Amendment to Credit Agreement]
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GENERAL ELECTRIC CAPITAL CORPORATION, as Agent

By:                /s/ Andrew D. Moore
Name:                    Andrew D. Moore
Title:                    Duly Authorized Signatory

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[Signature Page to Second Amendment to Credit Agreement]
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GE JV SPONSOR LTD, as a Lender

By: GENERAL ELECTRIC CAPITAL
CORPORATION, as Servicer

By:                /s/ Andrew D. Moore
Name:                    Andrew D. Moore
Title:                    Duly Authorized Signatory

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[Signature Page to Second Amendment to Credit Agreement]
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MDC JV SPONSOR LTD, as a Lender

By: GENERAL ELECTRIC CAPITAL
CORPORATION, as Servicer

By:                /s/ Andrew D. Moore
Name:                    Andrew D. Moore
Title:                    Duly Authorized Signatory

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[Signature Page to Second Amendment to Credit Agreement]
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SILICON VALLEY BANK,
as a Lender

By:                /s/ Peter Freyer
Name:                    Peter Freyer
Title:                    Director –Corporate Finance;  
Healthcare & Life Science

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[Signature Page to Second Amendment to Credit Agreement]
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BANK OF AMERICA, N.A.
as a Lender

By:                /s/ John C. Plecque
Name:                    John C. Plecque
Title:                    Senior Vice President

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[Signature Page to Second Amendment to Credit Agreement]
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CITIBANK, N.A,
as a Lender

By:                /s/ Alvaro De Valasco
Name:                    Alvaro De Valasco
Title:                    Vice President

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[Signature Page to Second Amendment to Credit Agreement]
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MORGAN STANLEY BANK, N.A,
as a Lender

By:                /s/ Alice Lee
Name:                    Alice Lee
Title:                    Authorized Signatory

[Signature Page to Second Amendment to Credit Agreement]
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