[BioC] Affymetrix reannotation

[Samuel Wuest]

Thanks a lot,

I am familiar with the ath1121501 package. Now I don’t know whether it 
contains informations on the probe-level rather than on the probeset-level 
(e.g. whether a designed probe still targets an updated gene model? or which 
probe-sets are obsolete and can be considered to be outdated?)

And: How can I retrieve such information without writing a blast-script to 
check every single probe against the most updated cDNA database?

Thanks for any help on this.
Samuel

On Tue, 06 Nov 2007 10:31:38 -0800
  Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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
>