[BioC] heatmap

[kfbargad@ehu.es]

Thanks for your answer Kevin,

I used the default option, which I think is euclidean (is this what 
you call absolute?) since heatmap uses dist() arguments. I checked 
?dist and found that Spearman and Pearson (which are the ones that I 
am most familiar with) were not among the options for distance 
measures. Is there a reason for this? maybe they can be found elswhere?

David

> What are you using as the measure of similarity? If you use absolute 
> correlation, then things that are highly negatively correlated 
(since 
> they have opposite expression patterns) should cluster together.
> 	Kevin
> 
> kfbargad at ehu.es wrote:
> > Dear list,
> > 
> > I have obtained a heatmap from my list of significant genes using 
the 
> > function heatmap(). I enclose an image of it. The sequences are 
> > coloured using maPalette().
> > 
> > I was confused when looking at the gene tree structure, some of 
the 
> > sequences that are coloured in red on the left hand side of the 
tree
> > (hopefully because of their high 
> > intensity) cluster together with some of the sequences that are 
> > coloured in green on the same samples. Should I not see the "red-
on-
> > the-left-group/green-
> > on-the-right-group" sequences all clustered together on one big 
branch 
> > of the genetree, and the "green-on-the-left-group/red-on-the-right-
> > group" sequences on another big branch? In a different way, why 
would 
> > a sequence cluster tightly together with others that have a 
completely 
> > swapped colour profile across samples?
> > 
> > Hope I make myself understandable
> > 
> > Best,
> > 
> > David
> > 
> > 
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