[BioC] Plotting Gene Expression Values
sdavis2 at mail.nih.gov
Sun Mar 6 00:34:53 CET 2005
----- Original Message -----
From: "McGee, Monnie" <mmcgee at mail.smu.edu>
To: <bioconductor at 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?
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:
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.
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