XPS package working with Affymetrix GeneChip 1.0 ST at gene level

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Guest User ★ 13k

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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.

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ADD COMMENT • link updated 12.6 years ago by cstrato ★ 3.9k • written 12.6 years ago by Guest User ★ 13k

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Benilton Carvalho ★ 4.3k

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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

ADD COMMENT • link 12.6 years ago Benilton Carvalho ★ 4.3k

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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

ADD REPLY • link 12.6 years ago Groot, Philip de ▴ 630

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cstrato ★ 3.9k

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Last seen 6.2 years ago

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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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