[BioC] Affymetrix MASv5 code & sample data

[Mike Lelivelt]

We have a PLIER technical note that has been awaiting clearance for sometime
now.  I'm checking on its status.  I'll post when it's up. Yes, I agree that
method docs are critical.

On a separate note, the PLIER SDK as it currently exists does not include
any normalization processing on the front end or variance stabilization on
the back end (PLIER + 16).  We are considering extending this functionality,
but resources have been tight.

 mike


On 6/9/05 10:45 AM, "Adaikalavan Ramasamy" <ramasamy at cancer.org.uk> wrote:

> Thank you for making the source codes available.
> 
> While on the subject I like to ask that if there is a documentation
> describing how the PLIER algorithm works. I think some sources point to
> the main Affymetrix website but I was unable to find it a few weeks
> back. 
> 
> Can you give me the explicit link to a document about PLIER please ?
> 
> BTW, the white paper entitled "Statistical Algorithms Description
> Document" was pretty good at explaining what MAS 5.0 did and I was
> hoping that it might be updated or modified to explain PLIER.
> 
> Thank you.
> 
> Regards, Adai
> 
> 
> On Wed, 2005-06-08 at 12:52 -0700, Mike Lelivelt wrote:
>> Dear Bioconductor Community:
>> 
>> I wanted to let everyone know that Affymetrix released the source code to
>> the MASv5 statistical algorithm several months back.  It is licensed under
>> the GNU:GPL.  You are welcome to access the code at the following URL below.
>> This URL also lists our ANSI C++ file parsers under LGPL and the PLIER code
>> under a GPL.  If our lawyers continue to agree, we should be making more
>> contributions to these code bases as well as new code bases under open
>> source licenses in the future.
>> 
>> http://www.affymetrix.com/support/developer/open_source/index.affx
>> 
>> Also you can find many sample datasets associated with a wide variety of
>> Affymetrix arrays at our developers network data resource center, as well
>> as links to other sample data sets on our website as well as public data
>> sets.  Heres a link
>> http://www.affymetrix.com/support/developer/resource_center/index.affx
>> 
>> To receive the monthly Affymetrix developer newsletter, register at
>> http://www.affymetrix.com and ensure that your profile has specified to
>> receive developer network communication.
>> 
>> Thanks for your continued support and interest, mike
>> 
>> -- Mike Lelivelt, Ph.D., Senior Manager of Informatics Applications,
>> Affymetrix, Inc.
>> Mike_lelivelt at affymetrix.com, cell 608-239-6937, office 608-985-6440  msg
>> sent from OS X
>> 
>> 
>> 
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>> 
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-- Mike Lelivelt, Ph.D., Senior Manager of Informatics Applications,
Affymetrix, Inc. 
Mike_lelivelt at affymetrix.com, cell 608-239-6937, office 608-985-6440 ­ msg
sent from OS X