[BioC] metadata - annotation package changes

[John Zhang]

>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
>> >> >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin 
>> >> (score=-3.906, 
>> >> >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99)
>> >> >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>> >> >> >Subject: [BioC] metadata - annotation package changes
>> >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch
>> >> >> >X-Mailman-Version: 2.1.6
>> >> >> >List-Id: The Bioconductor Project Mailing List 
>> >> <bioconductor.stat.math.ethz.ch>
>> >> >> >List-Unsubscribe: 
<https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
>> >> >> <mailto:bioconductor-request at stat.math.ethz.ch?subject=unsubscribe>
>> >> >> >List-Archive: <https://stat.ethz.ch/pipermail/bioconductor>
>> >> >> >List-Post: <mailto:bioconductor at stat.math.ethz.ch>
>> >> >> >List-Help: 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=help>
>> >> >> >List-Subscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
>> >> >> <mailto:bioconductor-request at stat.math.ethz.ch?subject=subscribe>
>> >> >> >Content-Transfer-Encoding: 7bit
>> >> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
>> >> >> pascal.dfci.harvard.edu
>> >> >> >X-Spam-Level: 
>> >> >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 
autolearn=ham  
>> >> >> version=3.0.1
>> >> >> >
>> >> >> >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