[BioC] affymetrix annotation

James W. MacDonald jmacdon at med.umich.edu
Mon Dec 20 21:58:12 CET 2010

Hi Arne,

On 12/20/2010 11:26 AM, arne.mueller at novartis.com wrote:
> Hello,
> 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 ...?

I doubt you are doing anything wrong. This may have changed a bit from 
the last time I talked to Marc, but in the past we needed a 'primary' 
mapping to start with, and chose the Affymetrix probeset ID --> Entrez 
Gene mapping that you can get from the latest Affy annotation file.

We assumed this to be the truth, and then did all the other mappings 
from Entrez Gene. The problem with this is that we are by definition 
using more dated information than you will typically get from Netaffx. 
So it is quite likely, given the fluid nature of this field, that some 
probesets will have different data in Netaffx than what you can get from 
the annotation packages.

As an aside, does this probeset have an Entrez Gene ID in the annotation 



>     thanks a lot for your help,
>     arne
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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