[BioC] hierarchical clustering - spearman correlation

Wolfgang Huber huber at ebi.ac.uk
Mon Nov 1 18:32:50 CET 2004

Liu, Xin wrote:
> Dear all,
> There are many libraries for the hierarchical clustering in R.
 > However, I can not find one hierarchical clustering by specifically
 > spearman correlation. Does any experienced guy provide some information?

Hi Xin,

you need to keep in mind that these are two separate things: calculation 
of the distance matrix (i.e. distance between each gene to every other 
gene), and the actual clustering algorithm to make this matrix into a 

You can use for example "cor" to calculate correlations including 
"pearson", "kendall", "spearman", and "hclust" to do the clustering.

Best wishes

> Thank you!
> Xin LIU
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Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber

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