[Bioc-devel] Updated annotation data for TESTING

Aedin aedin.culhane at ucd.ie
Wed Sep 7 16:18:58 CEST 2005

Sorry Robert.

I agree. My methods are pretty "old style", I tend to sort the platform
(GPL) number on GEO, bring down the list and just text extract it (Affy
u133a is GPL96).  On AE, the tend to put in the manufactory name and
guess (u133a is A-AFFY-33).
I've copied Tanya Barrett at GEO, and Helen Parkinson at AE in on this,
as I am sure they can point out how best to do this.


-----Original Message-----
From: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
Sent: 07 September 2005 14:52
To: Aedin
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] Updated annotation data for TESTING

Hi Aedin,
   These are all good suggestions. Do you happen to have code, or 
explicit instructions on how to obtain platform (ArrayExpress or GEO) in

an automated fashion? It seems like it could be pretty time consuming to

do this by hand.

   best wishes,

Aedin wrote:
> Dear Seth
> I know this can be inferred from the package name. But to make it 
> easier to browse the packages, would it be possible to a add a few 
> description columns to the metadata webpage.
> For example Organism/Species, platform (Affymetrix/ABI/Agilent/MWG 
> etc), type (microarray/CGH etc) and perhaps the number of 
> spots/probes. Also perhaps a platform (ArrayExpress or GEO) accession 
> number.  This would make it a lot easier to browse and find a specific
annotation package.
> Perhaps the simplest to implement would be to include an additional 
> chip name similar to the resourcerer chip names 
> (http://biocomp.dfci.harvard.edu/cgi-bin/magic/r1.pl).
> Thanks
> Aedin
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list 
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 981029-1024
rgentlem at fhcrc.org

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