Hi, a simple question I guess: I have 8 CEL files from U133A I run: library(affy) data<-ReadAffy() data2<-rma(data) data3<-exprs(data2) then: colnames(data3) and it start with the name of the first sample not with the probesetID If I run: dim(data3) I get: [1] 22283 8 Can I add this probeset column by doing this : tab <- data.frame(Name=geneNames(data2), data3) in this case dim(tab) gives me [1] 22283 9 which I like more...but am I right ? will it be the same with gcrma ? thanks Philippe

yes. and notice that rownames(data3) should give you the same thing as geneNames(data2) if you are interested in exporting use the method exprs2excel On Wed, 27 Aug 2003 Phguardiol@aol.com wrote: > Hi, > a simple question I guess: > I have 8 CEL files from U133A > I run: > library(affy) > data<-ReadAffy() > data2<-rma(data) > data3<-exprs(data2) > > then: > colnames(data3) > and it start with the name of the first sample not with the probesetID > > If I run: > dim(data3) > I get: > [1] 22283 8 > > Can I add this probeset column by doing this : > > tab <- data.frame(Name=geneNames(data2), data3) > > in this case dim(tab) gives me [1] 22283 9 which I like more...but am I right ? > will it be the same with gcrma ? > thanks > Philippe > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

If you want a data.frame, there is a generic method to cast 'exprSet' objects into data.frames (with the gene names and the covariate information in 'phenoData'). (note: it could require a 'devel' version of Biobase to work) Just do (in your example): tab <- as.data.frame(data2) Hopin' it helps, L. On Wed, Aug 27, 2003 at 01:49:16PM -0400, Phguardiol@aol.com wrote: > Hi, > a simple question I guess: > I have 8 CEL files from U133A > I run: > library(affy) > data<-ReadAffy() > data2<-rma(data) > data3<-exprs(data2) > > then: > colnames(data3) > and it start with the name of the first sample not with the probesetID > > If I run: > dim(data3) > I get: > [1] 22283 8 > > Can I add this probeset column by doing this : > > tab <- data.frame(Name=geneNames(data2), data3) > > in this case dim(tab) gives me [1] 22283 9 which I like more...but am I right ? > will it be the same with gcrma ? > thanks > Philippe > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently unspecified location -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent