Hi all,
I was wondering if there is any method implemented in bioconductor for
the analysis of Affymetrix Exon Arrays.
I used the exonmap package & affy tools to get RMA summarized
expression values, but there are aboud 1.4 milions probesets,
which is a bit too much to test while controling the FDR.
Is there a way to get a gene level index so that I can test about 20
000 genes rather than 1.4 milion probestes. I am not interested in
alternative splicing but in gene expression.
Thanks,
Adi
Hi Adi
If you use the Affymetrix Power Tools you can specify the
"--meta-probesets" option and provide the location of one of the .mps
files that you can find on the Affymetrix webpage. Then it summarises
probeset levels into metaprobesets, which I understand is what you are
looking for.
The GeneRegionScan package has a wrapper for this use. Look for
getLocalMetaprobeIntensities.
Best regards
Lasse Folkersen
Karolinska Institute, Sweden
>
> ------------------------------
>
> Message: 9
> Date: Mon, 1 Jun 2009 15:27:27 -0400
> From: "Tarca, Adi" <atarca at="" med.wayne.edu="">
> Subject: [BioC] Affy Exon arrays
> To: "'bioconductor at stat.math.ethz.ch'"
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>
> Hi all,
> I was wondering if there is any method implemented in bioconductor
for the analysis of Affymetrix Exon Arrays.
> I used the exonmap package & affy tools to get RMA summarized
expression values, but there are aboud 1.4 milions probesets,
> which is a bit too much to test while controling the FDR.
> Is there a way to get a gene level index so that I can test about 20
000 genes rather than 1.4 milion probestes. I am not interested in
alternative splicing but in gene expression.
>
> Thanks,
> Adi
>
>
Dear Adi
You may also look at BioC package xps, which is also able to summarize
exon arrays on both the probeset level and the transcript level.
Best regards
Christian
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