Hi Marco, Try this: (rmaData is an Expression-Set) cols <- palette(rainbow(ncol(exprs(rmaData)))) par(las=2,adj=1,cex=1,cex.axis=0.7) boxplot(as.data.frame(exprs(rmaData)),outline=F, col=cols, main="Boxplot RMA") #boxplot(as.data.frame(exprs(rmaData)), col=cols, main="Boxplot RMA") To adapt the output: ?par -> Help for the parameters of par Best regards, Sylvia ------------------------------ Message: 12 Date: Wed, 26 Jul 2006 15:40:29 -0700 From: Marco Blanchette <mblanche@berkeley.edu> Subject: [BioC] Dist of exprSet object To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <c0ed3d6d.2a10%mblanche at="" berkeley.edu=""> Content-Type: text/plain Thank you all, Using bioclite to download the annotation fixed the problem. Now, I am getting into simpler R problem. I have an exprSet object of 4 arrays: > eset Expression Set (exprSet) with 18952 genes 4 samples phenoData object with 1 variables and 4 cases varLabels sample: arbitrary numbering My goal is to draw a boxplot of the 4 different samples. Surely I can do: >boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], exprs(eset)[,4], col=c(2,3,4,5)) But is there an easier way to do with without having to subscript each individual column? [right now I have only 4 but when I will have 20, I?ll get bored quite rapidly] Sorry if this sounds easy, I am still learning the basics of R Marco ______________________________ Marco Blanchette, Ph.D. mblanche at uclink.berkeley.edu Donald C. Rio's lab Department of Molecular and Cell Biology 16 Barker Hall University of California Berkeley, CA 94720-3204 Tel: (510) 642-1084 Cell: (510) 847-0996 Fax: (510) 642-6062 -- [[alternative HTML version deleted]]