[BioC] heatmaps and pearson correlation

[Wolski]

Hi!

If your data are in the matrix use cor.

cor returns you the correlation matrix.

use ?t (transpose)
to compute the simmilarities either for rows or for columns.

mydist<-as.dist(1-cor(mymatrix))

now you can pass it to hclust.


Hope it helps.


*********** REPLY SEPARATOR ***********

On 7/20/2004 at 4:27 PM Arne.Muller at aventis.com wrote:
Hello,
I'm trying to construct a heatmap by clustering two dimensions (genes, treatments) using pearson correlation for both the distances (1 - correlation). Unfortinately the hclust and dist methods don't provide the pearson as a metric for distances (is there any reason for this?).
Has anyone a hint on how to make hclust and heatmap to cluster both dimensions via pearson correlation?
        thanks a lot for help,
        Arne

Dipl. bio-chem. Eryk Witold Wolski    @    MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin       'v'
tel: 0049-30-83875219               /   \
mail: wolski at molgen.mpg.de        ---W-W----    http://www.molgen.mpg.de/~wolski


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