[BioC] hclust and (Eisen+ de Hoon) cluster3 program

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Dec 6 12:22:37 CET 2004


You will likely get different results from all clustering software, even
when using the same parameters.  This is because many arbitrary
decisions have to be made during a hierarchical cluster analysis and
different programmers will make those decisions in different ways.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Benjamin
Sent: 06 December 2004 11:05
To: Bioconductor Mailing List
Subject: [BioC] hclust and (Eisen+ de Hoon) cluster3 program

Hi all,

I have a problem with the R function 'hclust'. I have noticed 
differences in clustering when I use the 'centroid' cluster method with 
'hclust' and the cluster3 program (see M. Eisen and M. de Hoon).

Have you noticed some differences too ?

I use

hclust from library 'stats' (Built: R 2.0.1; i386-pc-linux-gnu; 
2004-11-15 15:56:06; unix)
cluster 3.0 using C Clustering Library version 1.25

Thanks a lot

Benjamin Haibe-Kains

PhD student in the Machine Learning Group (MLG)
Universite Libre de Bruxelles (ULB)
E-mail: bhaibeka at ulb.ac.be 

MicroArray Unity 
Institut Jules Bordet (IJB)
E-mail: benjamin.haibekains at bordet.be

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