[BioC] Question about heatmap

[James W. MacDonald]

Giovanni d'Ario wrote:
> Hello everybody
>  I'have a general question about the heatmap function. I'm clustering an 
> expression matrix with different dissimilarity measures. Correct if I'm 
> wrong but if I want to cluster the columns I have to scale the rows to 
> bring the genes to a common range, and this is apparently the default 
> behavior of heatmap (according to the option scale="row"). So I expected 
> to see different dendrograms,  setting scale="none", but there's no 
> change. It seems that the scaling only affects the plotting but not the 
> generation of dendrograms. Where's the mistake?
> Thank you in advance
> Best regards

Although it is common to do heatmaps for microarray data, this function 
is part of base R so this question is better asked on the R-help list.

If you take a look at the code for heatmap you can see that the scaling 
is done on the data after the call to hclust() - it is only there to 
make the color range reasonable for comparison purposes.

Best,

Jim


> 
> Giovanni d'Ario
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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