Affy Exon arrays
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Tarca, Adi ▴ 570
@tarca-adi-1500
Last seen 2.1 years ago
United States
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
affy exonmap affy exonmap • 886 views
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@lasse-folkersen-3485
Last seen 8.4 years ago
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'" > ? ? ? ?<bioconductor at="" stat.math.ethz.ch=""> > Message-ID: > ? ? ? ?<05F1F2150E331540ADFD78E2AE933A3B41ECDB0CD9 at MED- CORE05.med.wayne.edu> > Content-Type: text/plain; charset=us-ascii > > 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 > >
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cstrato ★ 3.9k
@cstrato-908
Last seen 4.3 years ago
Austria
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 _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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