Question: Affymetrix MASv5 code & sample data
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gravatar for Lelivelt, Mike
14.6 years ago by
Lelivelt, Mike50 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 developeršs network data resource center, as well as links to other sample data sets on our website as well as public data sets. Herešs 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@affymetrix.com, cell 608-239-6937, office 608-985-6440 ­ msg sent from OS X [[alternative HTML version deleted]]
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ADD COMMENTlink modified 14.6 years ago by Adaikalavan Ramasamy1.8k • written 14.6 years ago by Lelivelt, Mike50
Answer: Affymetrix MASv5 code & sample data
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gravatar for Adaikalavan Ramasamy
14.6 years ago by
Adaikalavan Ramasamy1.8k 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@affymetrix.com, cell 608-239-6937, office 608-985-6440 msg > sent from OS X > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Adaikalavan Ramasamy ramasamy@cancer.org.uk Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Wolfson College Annexe Tel : 01865 284 408 Linton Road, Oxford OX2 6UD Fax : 01865 284 424
ADD COMMENTlink written 14.6 years ago by Adaikalavan Ramasamy1.8k
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 >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> -- 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
ADD REPLYlink written 14.6 years ago by Lelivelt, Mike50
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