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

Ramon Diaz-Uriarte rdiaz at cnio.es
Mon Sep 13 15:36:01 CEST 2004


On Monday 13 September 2004 10:36, michael watson (IAH-C) wrote:
> 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

Oh, but that is one problem I was referring to: say you use UPGMA; then, you 
will get a dendrogram; then, you can make up any story. That was one of my 
concerns. Clustering gives you clusters, but most papers I've seen that "use" 
clustering do not seem to be overly concerned about how meaningful and 
repeatable those clusters are. 

Related to the above, and to clustering being over-sold, is the fact that very 
rarely does one find discussion in those papers about how the type of 
clustering algorithm affects the results, and how different clustering 
algorihms/different metrics, etc, can relate to the prior beliefs about the 
shape of clusters (or how different clustering algorithms are better to 
detect different patterns).

And finally, it is not always clear that the difference between exploratory 
and confirmatory is being made. We can read senteces such as "the clustering 
results show that there are two groups"... Well, in what sense and how do the 
results from some aglomerative clustering algorithm show that there are two 
groups (and not twenty)?

But, again, I do think clustering has a role for certain types of questions. I 
just think it is not the magic bullet to "let the data speak for themselves", 
and similar marketing hype.

Best,

R.

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

-- 
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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