>Can you remember roughly when the previous time that you
>extracted the accession numbers from the Affymetrix files was?
I believe it was before June 2004. Check the date of build for 1.5.
>
>
>I keep asking because as far as I can tell, the Affymetrix
>Representative Public IDs have not changed since the first version
>of the annotation files that I have worked with, which was
>June 2004 (but I know that the first release of the Affy files was
March
>2003).
>I have asked Affymetrix whether the Representative Public IDs
>were static data or not, but I didn't get a very precise reply.
>
>Many thanks,
>Maria.
>
>
>On Wed, 10 Aug 2005, John Zhang wrote:
>
>> Date: Wed, 10 Aug 2005 08:17:13 -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: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at
stat.math.ethz.ch
>> Subject: Re: [BioC] metadata - annotation package changes
>>
>>
>> >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="">
>> >> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk
>> >> >> >To: bioconductor at stat.math.ethz.ch
>> >> >> >MIME-Version: 1.0
>> >> >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact
CCSG more
>> >> information
>> >> >> (
http://www.cryst.bbk.ac.uk/CCSG/)
>> >> >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean
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>> >> >> >Subject: [BioC] metadata - annotation package changes
>> >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch
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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
>> >>
>> >
>> >_______________________________________________
>> >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
