[BioC] Affymetrix reannotation

[James W. MacDonald]

Hi Samuel,

If you just want to ensure the probes in each probeset actually map to 
the current genome build, then you might consider the MBNI re-mapped 
cdfs. For the ath1121501 chip there are two you could consider; the 
ath1atrefseqcdf or ath1attaircdf packages.

The probes were first blasted against this version of the genome 
(1con.01222004, file date is 08/10/2006) -- not sure what that means, as 
I am not a plant guy. The probes that mapped to a single unique sequence 
on the genome were then annotated to genes using either TAIR or RefSeq 
(this is part of the package name above), so you are assured that any 
probes that are outdated have been removed.

More info is available here (note these are version 10):

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v10

You can get the package(s) in one of two ways. First, you can get them 
automagically by doing something like:

dat <- ReadAffy(filenames=list.celfiles(), cdfname="ath1atrefseqcdf")

or you can download/install using biocLite() and then specify in your 
call to ReadAffy() (or justRMA()/justGCRMA() if you are going that route).

Best,

Jim

Samuel Wuest wrote:
> 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 probe-sets are obsolete and can be considered to be outdated?)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
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
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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
>>
> 
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623