[BioC] recipe for heatmap

Marc Salit salit at nist.gov
Fri Jul 2 15:45:10 CEST 2004

Hi all --

I've data from 12 affy arrays, 5 in one class, 7 in the other. I am 
looking for genes that classify a sample into one or the other classes.

One thing I'd like to do is to be able to visually evaluate the power 
that exists to distinguish the classes, using clustered heatmaps. I've 
done some of this in the dchip program and NCI's BRB arraytools, but I 
haven't found an appropriate vignette or lab/tutorial example in the R 

I am guessing that I need to filter the genes to those that are 
differentially expressed, then use the 'heatmap' function. One thing I 
can't see immediately is how to identify the different classes in the 
call to heatmap...

I'm certain that I'm not the first to tackle this, can someone share 
their experience?

Thanks in advance!

Dr. Marc Salit
Research Chemist
Chemical Science and Technology Laboratory
100 Bureau Drive, Stop 8391
Gaithersburg, MD 20899-8391
email: Salit at NIST.gov
voice: +1 301 975-3646
fax:   +1 301 869-0413

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