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

Tan, MinHan MinHan.Tan at vai.org
Mon Dec 6 22:25:46 CET 2004

Did you use a correlation distance metric for hclust? 

AFAIK, that's what the Eisen software uses. I think the default distance
metric for hclust is Euclidean?

Could be wrong, but it's worth a try.

Min-Han Tan

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Benjamin
Sent: Monday, December 06, 2004 7:10 AM
To: Bioconductor Mailing List
Subject: Re: [BioC] hclust and (Eisen+ de Hoon) cluster3 program

Hi Michael,

I think that the differences are  too important to be due to different 
implementation decisions. Actually my problem is that I have a group of 
1 object and the rest in the other group when I use the 'centroid' 
hclust (I use cutree to have the main two groups)  and it's not the case

with other softwares. It looks like a bug in the Fortran routine but I 
can not access to it.

Have you reported this "bug" before ? Can I write my 'centroid' method 
easily ?



michael watson (IAH-C) wrote:

>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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