[BioC] metadata - annotation package changes

[John Zhang]

>OK, but what release  of the Affymetrix csv files 
>was used for the previous annotation packages,
>and which field of the csv files did the accession numbers come from?

We did not keep the information back then as it was a little hard to extract the 
dates for the files programmatically from Affymetrix web site. Should be on the 
to do list. 

The field for accession numbers is "Representative Public ID"


>
>Thanks for trying to answer my question.
>Maria.
>
>
>On Tue, 9 Aug 2005, John Zhang wrote:
>
>> Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT)
>> From: John Zhang <jzhang at jimmy.harvard.edu>
>> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk
>> Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk
>> Subject: Re: [BioC] metadata - annotation package changes
>> 
>> http://www.affymetrix.com/support/technical/byproduct.affx?
>> 
>> >If you were involved with building the previous releases you can probably 
>> >tell me where the 
>> >accession numbers for the previous releases (1.5,1.6,1.7)
>> >came from.
>> >Do you actually get them from the Affymetrix annotation files, 
>> >and if so, which section? For some probe sets different sections
>> >of the Affymetrix files give different accession numbers.
>> 
>> CSV files for chips under 
>> http://www.affymetrix.com/support/technical/byproduct.affx?
>> 
>> 
>> >
>> >Many thanks,
>> >Maria.
>> >
>> >
>> >On Tue, 9 Aug 2005, John Zhang wrote:
>> >
>> >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT)
>> >> From: John Zhang <jzhang at jimmy.harvard.edu>
>> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk
>> >> Subject: Re: [BioC] metadata - annotation package changes
>> >> 
>> >> Although I was involved in building 1.8, Seth is probably the best one to 
>> answer 
>> >> this question. My understanding is that, correct me Seth if I am wrong, a 
set 
>> of 
>> >> fresh base files (probe id to GeneBank accession number mappings extracted 
>> from 
>> >> Affymetrix) were used to build the new version of annotation packages.
>> >> 
>> >> 
>> >> 
>> >> >X-Original-To: jzhang at jimmy.harvard.edu
>> >> >Delivered-To: jzhang at jimmy.harvard.edu
>> >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST)
>> >> >From: Maria Stalteri <m.stalteri at mail.cryst.bbk.ac.uk>
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>> >> >
>> >> >Hi,
>> >> >I guess my question is mainly directed to John Zhang and
>> >> >the other authors/maintainers of the annotation packages
>> >> >for Affymetrix chips.
>> >> >
>> >> >In the latest versions (1.8) of the moe430a and rae230a
>> >> >packages, the probe set ID-to-accession number mappings
>> >> >(ACCNUM) are different from those given in previous
>> >> >versions (1.5, 1.6, 1.7).
>> >> >
>> >> >Can someone please explain to me why there has been 
>> >> >a change?
>> >> >
>> >> >Regards,
>> >> >Maria.
>> >> >
>> >> >_______________________________________________
>> >> >Bioconductor mailing list
>> >> >Bioconductor at stat.math.ethz.ch
>> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> 
>> >> Jianhua Zhang
>> >> Department of Medical Oncology
>> >> Dana-Farber Cancer Institute
>> >> 44 Binney Street
>> >> Boston, MA 02115-6084
>> >> 
>> 
>> Jianhua Zhang
>> Department of Medical Oncology
>> Dana-Farber Cancer Institute
>> 44 Binney Street
>> Boston, MA 02115-6084
>>
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084