[BioC] heatmaps and pearson correlation

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Jul 20 16:31:07 CEST 2004

I don't have the exact code to hand, but as I recall heatmap() either
takes data and does the clustering itself, or it takes two pre-computed
trees, as from the output of hclust().  Therefore, you need to do two
hclust() operations to produce two trees, and then pass those trees as
arguments to heatmap().

	-----Original Message-----
	From: Arne.Muller at aventis.com [mailto:Arne.Muller at aventis.com] 
	Sent: 20 July 2004 15:28
	To: bioconductor at stat.math.ethz.ch
	Subject: [BioC] heatmaps and pearson correlation


	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, 


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