[BioC] metadata - annotation package changes

[Maria Stalteri]

The 1.5 packages were built in  March 2004.


On Wed, 10 Aug 2005, John Zhang wrote:

> Date: Wed, 10 Aug 2005 09:13:17 -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
> 
> 
> >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>
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> >> >> >> >Subject: [BioC] metadata - annotation package changes
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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
>