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

[Charles C. Berry]

On Mon, 6 Dec 2004, Benjamin Haibe-Kains wrote:

> 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.

Source code is available from CRAN. In

 	http://cran.r-project.org/src/base/R-2/R-2.0.1.tar.gz

the directory

 	R-2.0.0/src/library/stats/src

contains hclust.f and hclust-utils.c.

Happy debugging.

;-)


>
> Have you reported this "bug" before ? Can I write my 'centroid' method easily 
> ?
>
> cheers,
>
> benjamin
>
> michael watson (IAH-C) wrote:
>
>> Benjamin
>> 
>> 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.
>> 
>> Mick
>> 
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Benjamin
>> Haibe-Kains
>> 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
> [http://www.ulb.ac.be/di/map/bhaibeka/]
>
>
> PhD student in the Machine Learning Group (MLG)
> 	[http://www.ulb.ac.be/di/mlg/]
> Universite Libre de Bruxelles (ULB)
> E-mail: bhaibeka at ulb.ac.be 
> MicroArray Unity 	[http://www.bordet.be/servmed/array/index.htm]
> Institut Jules Bordet (IJB)
> E-mail: benjamin.haibekains at bordet.be
>
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>

Charles C. Berry                        (858) 534-2098
                                          Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://hacuna.ucsd.edu/members/ccb.html  La Jolla, San Diego 92093-0717