[BioC] which package to cluster microarray data?

[David Ruau]

Hi Alessandro,

You can use the function hclust from the stats package (loaded by  
default)
 > ? hclust

For the uncentered pearson correlation use cor.dist() from the  
bioDist package
 > library(bioDist)
 > ?cor.dist

To perform your clustering with the UPGMA use hclust(d,  
method="average")
And if you want to have a heatmap of your cluster:
 > library(simpleaffy)
 > heatmap(eset, col= blue.white.red.cols, cor.dist,  
hclustfun=function(c){hclust(c,method='average')})

Best,
David

---
David Ruau
Institute for Biomedical Engineering
RWTH Aachen

On Sep 19, 2007, at 3:39 PM, Alessandro Fazio wrote:

>
> Hello!
>
> I would like to perform a cluster analysis by using UPGMA  
> (unweighet pair-group average) with a non-centic Pearson  
> correlation based distance. Does someone know which package I could  
> use to have "this desire" satisfied?
>
> Thank you in advance
>
> Alessandro
> _________________________________________________________________
> [[replacing trailing spam]]
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/ 
> gmane.science.biology.informatics.conductor