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
> _________________________________________________________________
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> gmane.science.biology.informatics.conductor
Hi Alessandro,
besides hclust you may also look at the package pvclust
www.is.titech.ac.jp/~shimo/prog/pvclust/ and
cran.r-project.org/doc/packages/pvclust.pdf)
Just note that the bootstrap calculations take a lot of time !
Wolfgang
Alessandro Fazio a ?crit :
> 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
> _________________________________________________________________
>
>
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
. . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et G?nomique Int?gratives
IGBMC
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger at igbmc.u-strasbg.fr
