[BioC] heatmap

[kfbargad@ehu.es]

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