[BioC] recipe for heatmap

Laura Hollins LHollins at PICR.man.ac.uk
Fri Jul 2 16:09:36 CEST 2004

Hi Marc,

I've used the 'heatmap' function to display differential genes. I
filtered my data first using simpleaffy, and then created a heatmap as
in the example below:

>exprs.eset <- exprs(eset)			#to get expression
values from normalised expression set
>heatmapgenes <- exprs.eset[filtered,]	#to get just the values for my
differential genes
>samplenames <- as.vector(eset$class)	#to get the names of the classes
into a vector
>colnames(heatmapgenes) <- samplenames	#this allows you to label your
samples by class in the heatmap

If you alter the 'samplenames' vector, you can alter the labels on the
heatmap. You can also do this with the argument 'labCol'.

Hope this helps,



Laura Hollins

PhD Student 
Bioinformatics Group 
Paterson Institute for Cancer Research 

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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