[BioC] Affymetrix annotation package

[Lapointe, David]

I've noticed some discrepancies with annotations, also. At least for
human, GeneCards has links from affy_id to other useful data. It is
somewhat manual, though.

Example:
http://rcdev.umassmed.edu/cgi-bin/genecards/carddisp.pl?gene=POLE&search
=1726_at&suff=txt




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W.
MacDonald
Sent: Tuesday, July 31, 2007 9:27 AM
To: Hans-Ulrich Klein
Cc: Bioconductor list
Subject: Re: [BioC] Affymetrix annotation package

Hi Hans,

Did you try Google? I find the first item on that list to be pretty
informative.

Best,

Jim



Hans-Ulrich Klein wrote:
> Dear list,
> 
> I wonder about the annotation of some probesets on Affymetrix chips.
E.g.:
> 
>> library("hgu95av2")
>> get("1726_at", env=hgu95av2ACCNUM)
> [1] "HG919-HT919"
> 
> Is "HG919-HT919" really an accession number? I do not get any hits at
NCBI's GenBank. NetAffx gives the same identifier for that probeset, but
in a field called "Representative Public ID".
> There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the
hgu95av2 chip. Where can get more information about this identifiers?
> 
> Thanks,
> Hans-Ulrich
> 
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

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