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

[Benjamin Haibe-Kains]

Thanks for the link to the source code, I will look it into details.

For the distance, I use the same one in hclust and eisen, i.e. the 
pearson correlation (also called uncentered correlation). Moreover, I 
use the 'median center' normalization.

benjamin

Charles C. Berry wrote:

> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>
> 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
>
>
>

-- 
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