[BioC] heatmap

[Carlos J. Gil Bellosta]

Yes, there is a reason. In fact, if the arrays v and w are normalized
(mean(v) = mean(w) = 0, sd(v) = sd(w) = 1), then the euclidean distance
between w and v is, in fact, 2 - 2 cor(u, v). The closer cor(u,v) is to
1, the smaller the euclidean distance...

Carlos J. Gil Bellosta
http://www.datanalytics.com 

El lun, 06-02-2006 a las 17:43 +0100, kfbargad at ehu.es escribió:
> 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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