[BioC] difference between annotation

Michal Okoniewski MOkoniewski at PICR.man.ac.uk
Fri Dec 15 12:04:38 CET 2006

Hi Greg. 

It is not too surprising - there are 11-16 probes in a probeset and sometimes some of them may match other genes/transcripts than intended initially by Affy. 
Thus the structure of annotations is not as simple as a probeset-gene pairs. There is also a number of papers on evolving annotations - the databases like Ensembl are not stable - transcripts/ESTs come and go... 
That's why you can rely on annotations only in an approximate way. 
If you want to be sure - map (e.g. blast) the probes yourself - then you have much more control on what is targeted by the probeset or check something like our web apps :


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of gregory voisin
Sent: 14 December 2006 20:15
To: bioconductor
Subject: [BioC] difference between annotation

Hi Bioconductorians!!!!

I work with HGU133.2.plus

I would like why there is a difference between annotation got limma in and Affymetrix's annotation??????

because sometimes for a probeset given , the limma's annotation gives on information and affymetrix gives another information......

(( Moreover, I add  that the annotation of Pathway Assist are too different ( AROUND 15 TO 20 %)AND THE STRATAGENE'S TEAM (PRIVATE COMPANY) ARE VERY GOOD  IN BUSINESS BUT NOT VERY GOOD IN RELATIONSHIP  .... it will be to get a consensus , one day .....))





 interface révolutionnaire.

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