[BioC] Group samples on heatmap?

[James W. MacDonald]

Hi Michael,

Michael Imbeault wrote:
> Is there a way to group samples and display them on an heatmap? Im using 
> the simpleaffy package to analyze some Affymetrix data - we have 12 
> chips, 6 from each donor (A and B) at different time points / treatments.
> 
> Im using hmap.pc to build an heatmap out of a filtered paircomp object, 
> but would want to display the mean of the 2 donors for each treatment / 
> time pair (so 6 samples total) instead of each chip on the heatmap.
> 
> Can this be done?

I can't speak for hmap.pc, as I don't know what package that is in. 
However you could use either heatmap or heatmap.2 in the gplots package 
to do the heatmap, in which case you would simply compute the mean of 
the samples and feed that as input to the heatmap function.

Presumably you would be able to do the same for hmap.pc, but as I 
mentioned, I don't know that function.

Best,

Jim

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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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