[BiO BB] Re: question on clustering

[Dan Bolser]

I tried to get a 'community answer' page going at...

http://en.wikipedia.org/wiki/Sequence_clustering

but it dosen't explicitly deal with similarity matrix clustering
techniques.

Please feel free to contribute!

Dan.

On Fri, 6 Aug 2004, William Thompson wrote:

>You might want to look into R http://www.r-project.org/ R is a programming tool 
>for statistics and data analysis. R has a fairly complete clustering package. 
>It's free, robust and there are lots of web resources for it.
>
>Bill
>
>Bill Thompson, PhD
>Bioinformatics Center
>NYS Department of Health
>Center for Medical Science, rm 2006
>150 New Scotland Avenue
>Albany, New York 12208
>(518) 486-7882
>
>
>
>> Hi all,
>> 
>> I have a question that concerns my MSc project. I am trying to cluster 30
>> CCP-modules (Complement Receptor 1) after having used a novel approach that
>> looks at the electrostatic surfaces. I have reached the stage where I have
>> obtained a similarity matrix of 30 by 30 filled with positive scores. The
>> higher a score the more similar two modules are. For example, if matrix entry
>> (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than
>> to module 6 due to a higher score. My problem now is to cluster these 30
>> modules based on this one similarity matrix. I am not used to have to cluster
>> small datasets or in this case a similarity matrix and not having training
>> data. I have searched around a lot on Google for programs that could cluster 
>my
>> modules using the similarity matrix but so far I have not found anything very
>> helpful. Does anyone know of a program (preferably free software) that could
>> help me out here, or another way which I could easily implement myself in a
>> script, that would be valid? I would really appreciate all replies to this
>> message and thank you all already for looking at this and thinking about this.
>> 
>> Thanks and regards,
>> Floris
>
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