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

[cstrato]

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.

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
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>> 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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> 
> 
>