[BioC] Affymetrix reannotation

[Samuel Wuest]

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