[BioC] Re: [S] Error in clustering procedure

[michael watson (IAH-C)]

I guess I'm coming to this late, but I'm pretty sure all biologists use cluster analysis for is for finding out which genes are behaving similarly to one another in a large data set.  Then if, for example, all genes from a certain pathway are showing a similar expression pattern, we have a hypothesis which can be tested further.

If cluster analysis has indeed been "over-sold", please suggest a better algorithm for summarising groups of genes that are behaving similarly across a group of experiments or time-points :-)

M

-----Original Message-----
From: Ramon Diaz-Uriarte [mailto:rdiaz at cnio.es] 
Sent: 08 September 2004 09:33
To: bioconductor at stat.math.ethz.ch
Cc: Prof Brian Ripley; cstrato; James W. MacDonald
Subject: Re: [BioC] Re: [S] Error in clustering procedure


On Tuesday 07 September 2004 21:17, cstrato wrote:
> Dear all
>
> First of all, I want to apologize to Prof. Ripley, since I forgot to 
> ask him first for permission to publish his comment.
>
> Personally, I agree that this would be useless, as Prof. Ripley has 
> already told me some years ago. However, almost everybody still seems 
> to do it and publish the corresponding results. Companies such as 
> Spotfire are proud that you can do hierarchical clustering with more 
> than 20,000 genes. I have never seen a publication where it was done 
> differently.


Part of this could be the result of imitative behavior, beliefs that "unless I 
put a neat heatmap I won't get it past reviewers", etc, but not evidence that 
it is the best way to go. If several companies are making an issue out of it 
in their brochures, maybe it is because customers ask for clustering.  As for 
"publish the corresponding results" I am not sure what the "results" are, 
since after clustering 7000 genes you can almost always make up a story after 
the fact; but I would not call that a result. 

I think clustering (and biclustering) do have a place, but I guess they should 
be used as a tool to answer some question (e.g., I think I understand what 
question a t-test is helping to answer; I am not sure about most clustering 
procedures), or as a guidance for something, not as some kind of magic tool 
to "let the data speak for themselves" ( = a) get the microarray data; b) run 
a clustering procedure; c) come up with a question that your cluster 
"answered".)

R.


>
> I think that the bioconductor list would be the best forum to discuss 
> this issue, and provide solutions (besides the obvious suggestion to 
> filter non-varying genes).
>
> Best regards
> Christian
>
> James W. MacDonald wrote:
> > cstrato wrote:
> >> Sorry, but I cannot resist:
> >>
> >> Any comments of the microarry community on the usefulness of 
> >> hierarchical clustering of 7000 genes?
> >
> > I think this would be almost completely useless. First off, 
> > clustering is not an inferential technique, so its use has been 
> > completely oversold IMO to the biological community. Secondly, 
> > clustering is usually done to produce a 'heat map' to put in a paper 
> > or flash on the screen during a presentation. How on earth would 
> > this be of any use? You couldn't even read any of the gene names!
> >
> > Of course you could use the heatmap to impress friends and 
> > colleagues with the fact that you rate a computer powerful enough to 
> > *do* a heatmap with a 7000 x 5 matrix ;-D
> >
> > Jim
> >
> >> Best regards
> >> Christian
> >> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> >> C.h.r.i.s.t.i.a.n. .S.t.r.a.t.o.w.a
> >> V.i.e.n.n.a.         .A.u.s.t.r.i.a
> >> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)

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