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                                                                    Exhibit 4.6

                           RESTRICTED STOCK AGREEMENT


     AGREEMENT made this 29th day of September, 2000, between AFFYMETRIX, INC.,
a Delaware corporation (the "Company"), CYRUS HARMON (the "Employee") and HARMON
FAMILY INVESTORS, LLC ("HFI LLC").

     For valuable consideration, receipt of which is acknowledged, the parties
hereto agree as follows:

     1.   EXCHANGE OF SHARES. In connection with the merger of Neomorphic, Inc.
(the "Seller") with and into a wholly owned subsidiary of the Company (the
"Merger") pursuant to that certain Agreement and Plan of merger dated as of
September 29, 2000 (the "Merger Agreement"), the Employee and HFI LLC will be
issued shares of common stock, par value $.01 per share, of the Company (the
"Common Stock") in exchange for all of his/its shares of capital stock of the
Seller in accordance with the terms of such agreement. Subject to the
consummation of the Merger, each of the Employee and HFI LLC has agreed that
two-thirds of the total number of shares of Common Stock received by the
Employee and HFI LLC in the Merger, including as a result of any adjustment to
the Common Conversion Ratio (as defined in the Merger Agreement) pursuant to
Section 1.5(d) of the Merger Agreement (such total number of shares, the
"Shares"), shall be subject to the purchase option set forth in Section 2 of
this Agreement and the restrictions on transfer set forth in Section 4 of this
Agreement (the shares subject to such restrictions, hereinafter referred to as
the "Restricted Shares").

     2.   PURCHASE OPTION.

     (a)  In the event that the Employee ceases to be employed by the Company as
a result of having been terminated by the Company for Cause (as defined below)
or if the Employee terminates his employment for any reason other than Good
Reason (as defined below), prior to the second anniversary of the date hereof,
the Company shall have the right and option (the "Purchase Option") to purchase
from each of the Employee and HFI LLC, for a sum (the "Option Price") of $0.10
per share divided by the Common Conversion Ratio (assuming that such ratio is
adjusted even if the Company exercised the Cash Option (as defined in the Merger
Agreement)), some or all of the Unvested Shares (as defined below). For the
purposes of this Agreement, the term "Cause" means: (1) the Employee's repeated
failure, after written notice thereof (describing in reasonable detail such
failure) and a 30-day period following the notice to cure such failure, to
perform his assigned duties and responsibilities as an employee of the Company
other than due to death or disability; (2) commission by the Employee of an
action which constitutes intentional misconduct or a knowing violation of law if
such action in either event results either in an improper substantial personal
benefit or a material injury to the Company; (3) the Employee's deliberate
disregard of material rules, regulations, instructions, personnel practices and
policies of the Company (as amended from time to time in the Company's sole
discretion) which results in material loss, damage or injury to the Company; (4)
the Employee's material breach of the

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non-disclosure, non-solicitation and assignment provisions contained in this
Agreement or in any other agreement to which the Company and the Employee are
parties; or (5) the Employee's conviction of, or plea of guilty or nolo
contendre to, any crime which constitutes a felony in the jurisdiction involved.
For the purposes of this Agreement, the term "Good Reason" means: (a) layoff or
involuntary termination of the Employee's employment, except in connection with
the termination of Employee's employment for Cause; (b) a material reduction by
the Company in the Employee's base salary or bonus eligibility, other than in
the case of reductions in salary or bonus eligibility with respect to similarly
situated employees of the Company generally; (c) mutual written agreement of the
Employee and the Board of Directors of the Company that Good Reason exists; (d)
the Employee being required by the Company to relocate to an office that is more
than 50 miles from Berkeley, California (other than the Company's offices
located in Santa Clara, California) without the consent of the Employee; (e) any
material breach by the Company or any successor thereto of any agreement to
which the Employee and the Company are parties, which breach is not cured within
thirty (30) days after written notice thereof; or (f) a material diminution in
the scope of the Employee's responsibilities or a change in the Employee's title
that is materially inconsistent with the Employee's responsibilities, in either
case without the consent of the employee.

     "Unvested Shares" means Shares that are not "Vested Shares." As of the
Effective Time (as defined in the Merger Agreement) and until the first
anniversary of the Effective Time (the "First Anniversary Date"), one-third of
the Shares shall be Vested Shares and two-thirds of the Shares shall be Unvested
Shares; from and after the First Anniversary Date and until the second
anniversary of the Effective Time (the "Second Anniversary Date"), two-thirds of
the Shares shall be Vested Shares and one-third of the Shares shall be Unvested
Shares; and from and after the Second Anniversary Date, all of the Shares shall
be Vested Shares and no Shares shall be Unvested Shares.

     (b)  In the event that the Employee's employment with the Company is
terminated by reason of death or disability or by the Company without Cause or
if the Employee terminates his/her employment for Good Reason, the Purchase
Option shall terminate and be of no further effect, the Company shall have no
right to purchase any of the Restricted Shares and any other restrictions or
conditions on the Restricted Shares pursuant to the Agreement shall be deemed
waived. For the purpose of this Agreement, "disability" shall refer to a
situation in which the Employee is totally disabled from performing his duties
for the Company during a period of six (6) consecutive months. If any question
shall arise as to whether during any period the Employee has suffered
disability, the Employee may, and at the request of the Company will, submit to
the Company a certification in reasonable detail by a physician selected by the
Employee or his guardian to whom the Company has no reasonable objection as to
whether the Employee was so disabled and such certification shall for the
purposes of this Agreement be conclusive of the issue. If such question shall
arise and the Employee shall fail to submit such certification, the Company's
determination of such issue shall be binding on the Employee.

     (c)  For purposes of this Agreement, employment with the Company shall
include


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employment with a parent, subsidiary or other affiliate of the Company.

     (d)  Notwithstanding anything herein to the contrary, the Board of
Directors of the Company (or a duly constituted committee thereof) shall retain
the ability to accelerate the vesting schedule specified in this Section 2 at
any time in its discretion.

     3.   EXERCISE OF PURCHASE OPTION AND CLOSING.

     (a)  The Company may exercise the Purchase Option by delivering or mailing
to the Employee (or his/her estate), within 30 days after the termination of the
employment of the Employee with the Company, a written notice of exercise of the
Purchase Option. Such notice shall specify the number of Restricted Shares to be
purchased. If and to the extent the Purchase Option is not so exercised by the
giving of such a notice within such 30 day period, the Purchase Option shall
automatically expire and terminate effective upon the expiration of such 30 day
period.

     (b)  Within 10 days after delivery to the Employee of the Company's notice
of the exercise of the Purchase Option pursuant to subsection (a) above, the
Employee (or his or her estate) and HFI LLC shall, pursuant to the provisions of
the Joint Escrow Instructions referred to in Section 6, tender to the Company at
its principal offices the certificate or certificates representing the Shares
which the Company has elected to purchase in accordance with the terms of this
Agreement, duly endorsed in blank or with duly endorsed stock powers attached
thereto, all in form suitable for the transfer of such Restricted Shares to the
Company. Upon receipt of such certificate or certificates, the Company shall pay
to the Employee and to HFI LLC their respective aggregate Option Prices for such
Restricted Shares.

     (c)  After the time at which any Shares are required to be delivered to the
Company for transfer to the Company pursuant to subsection (b) above, the
Company shall not pay any dividend to the Employee or to HFI LLC on account of
such Restricted Shares or permit the Employee or to HFI LLC exercise any of the
privileges or rights of a stockholder with respect to such Restricted Shares,
but shall, in so far as permitted by law, treat the Company as the owner of such
Restricted Shares. It being understood that, prior to the time at which any
Restricted Shares are required to be delivered to the Company for transfer to
the Company pursuant to subsection (b) above, the Company shall pay any and all
dividends or other distributions currently to the Employee and HFI LLC.

     (d)  The Option Price may be payable, at the option of the Company, in
cancellation of all or a portion of any outstanding indebtedness of the Employee
or HFI LLC to the Company or in cash (by check) or both.

     (e)  The Company shall not purchase any fraction of a Restricted Share upon
exercise of the Purchase Option, and any fraction of a Restricted Share
resulting from a computation made pursuant to Section 2 of this Agreement shall
be rounded to the nearest whole Restricted



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Share (with any one-half Restricted Share being rounded upward).

     4.   RESTRICTIONS ON TRANSFER.

     (a)  Neither the Employee nor HFI LLC shall sell, assign, transfer, pledge,
hypothecate or otherwise dispose of, by operation of law or otherwise, other
than by will or the laws of descent and distribution (collectively "transfer")
any Unvested Shares, or any interest therein, that are subject to the Purchase
Option, except that each of the Employee and HFI LLC may transfer such Shares to
or for the benefit of any spouse, child (natural or adopted) or grandchild, or
to a trust for their benefit, as applicable, PROVIDED that such Shares shall
remain subject to this Agreement (including without limitation the restrictions
on transfer set forth in this Section 4, and the Purchase Option) and such
permitted transferee shall, as a condition to such transfer, deliver to the
Company a written instrument confirming that such transferee shall be bound by
all of the terms and conditions of this Agreement.

     (b)  Notwithstanding anything in this Agreement to the contrary, the
parties hereto acknowledge and agree that each of the Employee and HFI LLC may,
at any time and without the prior consent of the Company, transfer any
Restricted Shares, or any interest therein, that are no longer subject to the
Purchase Option, subject to applicable law and any other agreements that the
Employee or HFI LLC may have with the Company.

     5.   ESCROW. Each of the Employee and HFI LLC shall, upon the execution of
this Agreement, execute Joint Escrow Instructions attached to this Agreement.
The Joint Escrow Instructions shall be delivered to State Street Bank and Trust
Company, as escrow agent thereunder. Each of the Employee and HFI LLC hereby
instructs the Company to deliver to such escrow agent, on behalf of the Employee
or HFI LLC, the certificate(s) evidencing the Restricted Shares subject to the
Purchase Option. Such materials shall be held by such escrow agent pursuant to
the terms of such Joint Escrow Instructions.

     6.   RESTRICTIVE LEGENDS. All certificates representing shares subject to
the Purchase Option shall have affixed thereto legends in substantially the
following form, in addition to any other legends that may be required under
federal or state securities laws:

     "The shares of stock represented by this certificate are subject to
     restrictions on transfer and an option to purchase set forth in a certain
     Restricted Stock Agreement between the corporation and the registered owner
     of these shares (or his or her predecessor in interest), and such Agreement
     is available for inspection without charge at the office for the Secretary
     of the corporation."

     7.   ADJUSTMENTS FOR STOCK SPLITS, STOCK DIVIDENDS, ETC.; MERGERS AND OTHER
SALE EVENTS.

     (a)  If from time to time there is any stock split, stock dividend, stock
distribution or


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other reclassification of the Common Stock of the Company, any and all new,
substituted or additional securities to which the Employee and HFI LLC are
entitled by reason of his/its ownership of the Unvested Shares shall be
immediately subject to the Purchase Option, the restrictions on transfer and the
other provisions of this Agreement in the same manner and to the same extent as
the Unvested Shares, and the Option Price shall be appropriately adjusted.

     (b)  In the case of and subject to the consummation of (i) the dissolution
or liquidation of the Company, (ii) the sale of all or substantially all of the
assets of the Company on a consolidated basis to an unrelated person or entity,
(iii) a merger, reorganization or consolidation in which the holders of the
Company's outstanding voting power immediately prior to such transaction do not
own a majority of the outstanding voting power of the surviving or resulting
entity immediately upon completion of such transaction, (iv) the sale of all of
the capital stock of the Company to an unrelated person or entity, or (v) any
other transaction in which the holders of the Company's outstanding voting power
immediately prior to such transaction do not own at least a majority of the
outstanding voting power of the relevant entity after the transaction (in each
case, regardless of the form thereof, a "Sale Event"), all Unvested Shares as of
the effective date of the Sale Event shall automatically become vested as of
such date, the Purchase Option shall be deemed terminated and of no further
effect and any other restrictions or conditions on the Shares pursuant to this
Agreement shall be deemed waived.

     8.   SECTION 83(b) ELECTION. Each of the Employee and HFI LLC acknowledges
that he/it has been informed of the availability of making an election in
accordance with 83(b) of the Internal Revenue Code of 1986, as amended; that
such election must be filed with the Internal Revenue Service within 30 days of
the transfer of shares to the Employee or HFI LLC, as the case may be; and that
the Employee and HFI LLC, as applicable, is solely responsible for making such
election. The Company agrees to take all reasonable actions to assist the
Employee and HFI LLC in determining an appropriate valuation of the Restricted
Shares for purposes of filing such election, including without limitation
providing access to any information useful in determining such valuation.

     9.   NON-COMPETITION.

     (a)  Employee acknowledges and agrees that by virtue of his previous
ownership interest in the Seller, he (1) has extensive knowledge of and access
to confidential information of the Company, (2) has benefited and would continue
to benefit greatly from Company goodwill, and (3) has had responsibilities
relating to all aspects of the business operations of the Company including, but
not limited to, those typically associated with the positions of President and
Chief Executive Officer, in all of the territories and geographical areas
covered by the Company's business operations. Employee further recognizes that
the Company based its decision to acquire the Seller largely on Employee's
representation that he would not compete with Company as provided herein.

     (b)  Accordingly, Employee agrees that, during the term of his employment
with the


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Company and for a period of one (1) year after the Effective Time of the Merger,
Employee shall not own, participate, engage, be employed by, contract with, or
have any interest in, directly or indirectly, the following companies and their
affiliates: PE Corp (Celera Genomics Group); Motorola, Inc.; Incyte Genomics,
Inc.; Hyseq, Inc.; Compugen Ltd; Rosetta Inparmatics, Inc.; Agilent
Technologies, Inc.; Corning, Inc.; Amersham Pharmacia Biotech; and DoubleTwist,
Inc.

     (c)  Employee acknowledges and agrees that his obligations not to compete
with the Company contained herein shall cover the activities of the Employee in
every part of the territories and geographical areas covered by the Company's
business operations.

     (d)  Each of the parties hereto acknowledges and agrees that the Employee's
obligations not to compete with the Company contained in this Section 9 shall be
construed as if each obligation is divided into separate and distinct
obligations in respect of the Company's business operations; each capacity in
which the Employee is prohibited from competing; each company and affiliate the
Employee is prohibited from owning, participating in, engaging with, being
employed by, contracting with, or having any interest in; and each part of the
territories and geographical areas covered by the Company's business operations.
Each such obligation shall constitute separate and several obligations distinct
from all other such obligations.

     (e)  Each of the parties hereto recognizes that the Employee's obligations
not to compete contained in this Section 9 are properly required for the
adequate protection of the Company's business operations and that in the event
any obligation or other provision contained herein shall be deemed illegal,
unenforceable, or unreasonable by a court or other tribunal of competent
jurisdiction with respect to any part of the obligation or provision, such
obligation or provision shall not be affected with respect to any other part of
the obligation or provision, and each of the parties hereto agrees and submits
to the reduction of the geographical area or list of companies and affiliates in
the provision or obligation as said court shall deem reasonable.

     (f)  Employee acknowledges and agrees that his obligations not to compete
with the Company contained herein constitute consideration not only under this
Agreement, but also for the Company's representations, warranties, covenants and
agreements set forth in the Confidential Information, Secrecy, and Invention
Agreement between the Employee and the Company.

     10.  NON-SOLICITATION. Employee recognizes and acknowledges that because of
his relationship with the Company it is essential for the protection of the
continuing business of the Company that Employee be restrained for a reasonable
period following the termination of Employee's employment with the Company from:
(1) soliciting or inducing any employee of the Company to leave the employ of
the Company; (2) hiring or attempting to hire any employee of the Company; or
(3) soliciting the trade of or trading with the customers of the Company for any
Competitive Business Purpose (as defined below). Accordingly, Employee agrees
that during the term of his employment with the Company, and for a period of one
(1) year following Employee's termination of employment with the Company, for
any reason whatsoever, Employee shall not, directly or indirectly, including,
but not limited to, whether on his own, with


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another, or in the supervision of another:

     (a)  hire, solicit, aid in or encourage the hiring and/or solicitation of,
contract with for employment or consulting or for any other purpose which is
competitive to the Company's business operation(s), or aid in or encourage such
contracting, or induce or encourage to leave the employment of the Company, any
employee of the Company; or

     (b)  hire, solicit, aid in or encourage the hiring and/or solicitation of,
contract with for employment or consulting or for any other purpose which is
competitive to the Company's business operation(s), aid in or encourage such
contracting, or induce or encourage to hire or cause to be hired, any individual
who has left the employment of the Company within one (1) year prior to the
termination of the Employee's employment with the Company; or

     (c)  hire, solicit, aid in or encourage the solicitation of, contract with,
aid in or encourage the contracting with, or contact any person or entity which
is, or was, within three (3) years prior to Employee's termination of employment
with the Company, any customer or client of the Company for the purpose of
offering or selling a product or service competitive with any of the Company's
businesses (a "Competitive Business Purpose").

     11.  INJUNCTION. Employee agrees that it would be difficult to measure any
damages caused to the Company which might result from any breach by the Employee
of the promises set forth in Sections 9 and 10, and that in any event money
damages would be an inadequate remedy for any such breach. Accordingly the
Employee agrees that if the Employee breaches, or threatens to breach, any
portion of Sections 9 or 10 of this Agreement, the Company shall be entitled, in
addition to all other remedies that it may have, to an injunction or other
appropriate equitable relief to restrain any such breach without showing or
proving any actual damage to the Company.

     12.  OWNERSHIP OF PRIOR DEVELOPMENTS. If at any time or times during the
Employee's performance of services for the Seller prior to the date hereof, the
Employee (either alone or with others) made, conceived, discovered or reduced to
practice any invention, modification, discovery, design, development,
improvement, process, software program, work of authorship, documentation,
formula, data, technique, know-how, secret or intellectual property right
whatsoever or any interest therein (whether or not patentable or registrable
under copyright or similar statutes or subject to analogous protection) that (a)
relates to the business of the Seller or any customer of or supplier to the
Seller or any of the products or services being developed, manufactured or sold
by the Seller or which may be used in relation therewith, (b) results from tasks
assigned to the Employee by the Seller or (c) results from the use of premises
or personal property (whether tangible or intangible) owned, leased or
contracted for by the Seller (each, a "Prior Development"), the Employee hereby
acknowledges that he has conveyed and assigned such Prior Developments to the
Seller and the benefits thereof are the sole and absolute property of the Seller
and its assigns, and to the extent that the Employee has not so conveyed and
assigned such Prior Developments to the Seller, the Employee hereby conveys and
assigns such Prior Developments to the Seller and acknowledges that the benefits
thereof are the sole and


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absolute property of the Seller and its assigns (subject to any rights that have
been granted by Seller to third parties, which rights are set forth on SCHEDULE
A attached hereto).

     13.  NO RIGHTS TO EMPLOYMENT. Nothing contained in this Agreement shall be
construed as giving the Employee any right to be retained, in any position, as
an employee of the Company.

     14.  SEVERABILITY. The invalidity or unenforceability of any provision of
this Agreement shall not affect the validity or enforceability of any other
provision of this Agreement, and each other provision of this Agreement shall be
severable and enforceable to the extent permitted by law.

     15.  WAIVER. Any provision for the benefit of the Company contained in this
Agreement may be waived, either generally or in any particular instance, by the
Board of Directors of the Company.

     16.  BINDING EFFECT. This Agreement shall be binding upon and inure to the
benefit of the Company, the Employee and HFI LLC and their respective heirs,
executors, administrators, legal representatives, successors and assigns,
subject to the restrictions on transfer set forth in Sections 4 and 5 of this
Agreement.

     17.  NOTICE. All notices required or permitted hereunder shall be in
writing and deemed effectively given upon personal delivery or five days after
deposit in the United States Post Office, by registered or certified mail,
postage fees prepaid, addressed to the other party hereto at the address shown
beneath his or its respective signature to this Agreement, or at such other
address or addresses as either party shall designate to the other by 10 days
advance written notice in accordance with this Section 17.

     18.  PRONOUNS. Whenever the context may require, any pronouns used in this
Agreement shall include the corresponding masculine, feminine or neuter forms,
and the singular from of nouns and pronouns shall include the plural, and vice
versa.

     19.  ENTIRE AGREEMENT. This Agreement and the Joint Escrow Instructions
attached hereto constitute the entire agreement between the parties, and
supersede all prior agreements and understandings, relating to the subject
matter of this Agreement.

     20.  AMENDMENT. This Agreement and the Joint Escrow Instructions attached
hereto may be amended or modified only by a written instrument executed by the
Company, the Employee and HFI LLC (and with respect to the Joint Escrow
Instructions only, with the consent of the Escrow Agent).

     21.  GOVERNING LAW. This Agreement shall be construed, interpreted and
enforced in accordance with the internal laws of the State of Delaware without
regard to any applicable


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conflicts of laws.

     22.  EFFECTIVENESS. Except for Section 12, which shall be effective on the
date first set forth above and shall remain effective regardless of any
termination of the Merger Agreement, the provisions of this Agreement shall be
effective only from and after the Effective Time and shall be of no force and
effect if the Merger Agreement is terminated in accordance with its terms.




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     IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of
the day and year first above written.

                                      AFFYMETRIX, INC.

                                      By: /s/ Susan E. Siegel
                                          Name: Susan E. Siegel
                                          Title: President


                                      Address:  3380 Central Expressway
                                                Santa Clara, CA  95051


                                      /s/ Cyrus Harmon
                                      Cyrus Harmon

                                      Address:  1805 Virginia St.
                                                Berkeley, CA  94703


                                      HARMON FAMILY INVESTORS, LLC



                                      By: /s/ Amy Harmon
                                          /s/ Cyrus Harmon
                                          Name: Amy Harmon, Cyrus Harmon
                                          Title: Managers


                                      Address: c/o Cyrus Harmon
                                               1805 Virginia St.
                                               Berkeley, CA  94703





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