XPS package working with Affymetrix GeneChip 1.0 ST at gene level
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Last seen 8.2 years ago
I was wondering if there is some way of getting the XPS package working at gene level as I need to get the gene expression from some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze. I tried to use the Affy package before but as far as I understand they need .CDF file to get working and I only have CLF and PBG files for my chips. Kind regards Jorge -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
cdf affy xps cdf affy xps • 800 views
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@benilton-carvalho-1375
Last seen 2.7 years ago
Brazil/Campinas/UNICAMP
Another alternative, given that the affy package is not designed for this, is the oligo package.... b On 2 June 2012 02:02, Jorge Mir? [guest] <guest at="" bioconductor.org=""> wrote: > > I was wondering if there is some way of getting the XPS package working at gene level as I need to get the gene expression from some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze. > > I tried to use the Affy package before but as far as I understand they need .CDF file to get working and I only have CLF and PBG files for my chips. > > Kind regards > Jorge > > ?-- output of sessionInfo(): > > - > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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I created some CDF-files for these chips that you can also use (not sure on the r4 though): http://nmg-r.bioinformatics.nl/NuGO_R.html Regards, Dr. Philip de Groot Bioinformatician / Microarray analysis expert Wageningen University / TIFN Netherlands Nutrigenomics Center (NNC) Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: "De Valk" ("Erfelijkheidsleer"), Building 304, Verbindingsweg 4, 6703 HC Wageningen Room: 0052a T: 0317 485786 F: 0317 483342 E-mail: Philip.deGroot at wur.nl I:???????? http://humannutrition.wur.nl https://madmax.bioinformatics.nl http://www.nutrigenomicsconsortium.nl -----Original Message----- From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: zaterdag 2 juni 2012 12:20 To: Jorge Mir? [guest] Cc: jorgma86 at gmail.com; bioconductor at r-project.org Subject: Re: [BioC] XPS package working with Affymetrix GeneChip 1.0 ST at gene level Another alternative, given that the affy package is not designed for this, is the oligo package.... b On 2 June 2012 02:02, Jorge Mir? [guest] <guest at="" bioconductor.org=""> wrote: > > I was wondering if there is some way of getting the XPS package working at gene level as I need to get the gene expression from some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze. > > I tried to use the Affy package before but as far as I understand they need .CDF file to get working and I only have CLF and PBG files for my chips. > > Kind regards > Jorge > > ?-- output of sessionInfo(): > > - > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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cstrato ★ 3.9k
@cstrato-908
Last seen 4.2 years ago
Austria
Dear Jorge, You can preprocess both, RaExon and RaGene 1.0 ST arrays, at the probeset and the gene level, simply set the option to either option="probeset" or to option="transcript", e.g.: data.rma <- rma(data.genome ,"RaGeneRMAMetacore", filedir=datdir background="antigenomic", normalize=TRUE, option="transcript", exonlevel="metacore+affx") See the help file ?rma. For further examples see the scripts "script4exon.R" and "script4xps.R" in the xps/examples directory. See also script "script4schemes.R" how to create the scheme for the RaGene array. 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 _._._._._._._._._._._._._._._._._._ On 6/2/12 3:02 AM, Jorge Mir? [guest] wrote: > > I was wondering if there is some way of getting the XPS package working at gene level as I need to get the gene expression from some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze. > > I tried to use the Affy package before but as far as I understand they need .CDF file to get working and I only have CLF and PBG files for my chips. > > Kind regards > Jorge > > -- output of sessionInfo(): > > - > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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