Exporting in XPS
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@lavorgna-giovanni-4817
Last seen 5.2 years ago
Dear all, before applying any filter to Exon data, I would like to export them to a text file as transcripts, i.e, I have RMAed my data using the following command following the code coming along with the package: rma.tc.core <- rma(data.exon, "MixExonRMAcore", filedir=outdir, tmpdir="", background="antigenomic", normalize=TRUE, option="transcript", exonlevel="affx+core") Is there a way to get an output like the following (also non log2 trasformed data will suffice): GeneID HCC1187 SUM44PE MCF7 MDAMB436 LY2 BT549 A1BG 6.31 6.35 6.66 6.47 6.81 6.66 A2M 4.37 4.58 4.57 4.44 4.84 4.47 A2ML1 5.50 5.85 5.54 5.53 5.60 5.31 A3GALT2 6.13 6.10 6.06 6.23 5.99 5.76 Thanks in advance. Giovanni ----------------------------------------------------------- Giovanni Lavorgna DIBIT-HSR Via Olgettina, 58 20132 Milan Italy Tel: +39-02-2643-4776 Fax: +39-02-2643-4767 Email: giovanni.lavorgna at hsr.it ---------------------------------------------------------------------- ---- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 info:www.5xmille at hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.6 years ago
Austria
Dear Giovanni, You can use function "export.expr()" which allows you to select the annotation you want using parameter "varlist". By default it is set to 'varlist="*"' which will export all annotation data. However, this will result in a huge file in the case of exon arrays, especially when using probesets. See the help file "?export.expr" For the transcript data "rma.tc.core" you can do: ds.tc <- export.expr(rma.tc.core, treetype="mdp", varlist="fUnitName:fTranscriptID:fSymbol:fLevel", outfile="MixExon_tc.txt", as.dataframe=TRUE) colnamesds.tc) pheno.tc <- ds.tc[,c("UnitName", "TranscriptID", "GeneSymbol")] expr.tc <- log2ds.tc[,5:ncolds.tc)]) rownamesexpr.tc) <- ds.tc[,"UnitName"] Here I have split the data into the annotation file "pheno.tc" and the log2 expression part "expr.tc". Now you can for example use both "pheno.tc" and "expr.tc" for package "limma". 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 7/25/12 7:02 PM, Lavorgna Giovanni wrote: > Dear all, > > before applying any filter to Exon data, I would like to export them to a text file as transcripts, i.e, I have RMAed my data using the following command following the code coming along with the package: > > rma.tc.core <- rma(data.exon, "MixExonRMAcore", filedir=outdir, tmpdir="", background="antigenomic", normalize=TRUE, option="transcript", exonlevel="affx+core") > > Is there a way to get an output like the following (also non log2 trasformed data will suffice): > > GeneID HCC1187 SUM44PE MCF7 MDAMB436 LY2 BT549 > A1BG 6.31 6.35 6.66 6.47 6.81 6.66 > A2M 4.37 4.58 4.57 4.44 4.84 4.47 > A2ML1 5.50 5.85 5.54 5.53 5.60 5.31 > A3GALT2 6.13 6.10 6.06 6.23 5.99 5.76 > > Thanks in advance. > > Giovanni > > > > > > ----------------------------------------------------------- > Giovanni Lavorgna > DIBIT-HSR > Via Olgettina, 58 > 20132 Milan Italy > Tel: +39-02-2643-4776 > Fax: +39-02-2643-4767 > Email: giovanni.lavorgna at hsr.it > -------------------------------------------------------------------- ------ > LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. > AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 > info:www.5xmille at hsr.it - www.5xmille.org > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > _______________________________________________ > 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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