[BioC] affymetrix annotation

Tim Yates TYates at picr.man.ac.uk
Mon Dec 20 22:29:10 CET 2010

We map to the Ensembl genome, so it's probably not what you are after, but we have the 430A arrays in xmap and you can search for probesets by entering their ids into the search box top right


How it's of some help...


----- Reply message -----
From: "arne.mueller at novartis.com" <arne.mueller at novartis.com>
Date: Mon, Dec 20, 2010 16:32
Subject: [BioC] affymetrix annotation
To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>


I was wondering where the mapping from affy probeset Ids to genes 
(EntrezGene) is coming from (package mouse4302.db). 
mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, 
what's the "original" link between an affy probeset and an EnterzGene Id, 
is it Netaffx? My problem is that I've an "interesting" probeset that is 
annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map 
contains NA for this probeset Id.

I'd be happy if someone could point me to some documentation how this 
annotation/mapping is derived or let me know what I'm doing wrong ...?

   thanks a lot for your help,

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