Dear BioC, I have completed an analysis of a set of microarray data (affy data), and I would like to plot the gene expression values. The purpose is to compare the genes in my four groups that are differentially expressed. I've done histograms and boxplots, but what I really want is a gene-by-gene comparison. How do I plot an expression set and how do I make sure that each of the expression values on the plot is labelled with the proper gene? Thanks, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035

----- Original Message ----- From: "McGee, Monnie" <mmcgee@mail.smu.edu> To: <bioconductor@stat.math.ethz.ch> Sent: Friday, March 04, 2005 3:49 PM Subject: [BioC] Plotting Gene Expression Values > Dear BioC, > > I have completed an analysis of a set of microarray data (affy data), and > I would like to plot the gene expression values. The purpose is to > compare the genes in my four groups that are differentially expressed. > I've done histograms and boxplots, but what I really want is a > gene-by-gene comparison. How do I plot an expression set and how do I > make sure that each of the expression values on the plot is labelled with > the proper gene? Monnie, You may want to look at ?heatmap. If you have your differentially expressed genes so that you can index your expression set, you can do: heatmap(exprs(MyExprs[diff.expressed.genes,])) This will give you the typical two-way clustering. You can use colors from the geneplotter package (dChip.colors or greenred.colors) to make a prettier picture. I prefer the heatmap.2 function from the gplots package (bundle gregmisc), but this will hopefully get you started. Sean