[BioC] Affymetrix reannotation

[Marc Carlson]

Samuel Wuest wrote:
> Hi,
>
> I trying to assess a modified version of the Affymetrix present/absent call 
> algorithm on my data, which have been generated from two-round amplified RNA 
> hybridized to the Arabidopsis ATH1 GeneChip.
>
> I would need some negative control probesets, and thought of probesets that 
> were designed based on wrong gene annotations (similar to what was used in 
> the PANP method from Peter Warren et al.).
> Therefore, I wondered whether someone does a reannotation of Affy probesets 
> on a regular base? (for example, the version 7 of the Arabidopsis Genome 
> Annotation has been released recently, and some probesets on the AffyChip 
> are most probably not matching any gene model anymore).
>
> If yes, where could I find the updated datafiles? Is there anything in the 
> BioC annotation package for the ATH1Chip?
>
> Thanks for any help.
> Best, Sam
>
> -----------------------------------------------------
> Dipl. Bot. Samuel Wust
> Dep. of Developmental Genetics
> Institute for Plant Biology
> University of Zuerich
> Zollikerstrasse 107
> CH - 8008 Zürich
> Phone: +41-(0)44 634 82 42
> Mobile: + 41 (0)76 501 69 22
> Email: swuest at botinst.uzh.ch
>
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>
>   

We provide a "standard" annotation package for this chip.  You can find
it here:

http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501.db.html


    Marc