[adegenet-forum] find.clusters without PCA

[Roberto Oliveira Santos]

Hi Federico

"shaming reputations"? sorry..., pretty much sure I don't have any
reputation :-) if anyone ask a naive question this should be response? I
disagree... anyway, thanks for the text. I'll keep in mind.

Cheers,

Roberto

2014-10-30 16:16 GMT+00:00 Federico Calboli <f.calboli at imperial.ac.uk>:

> You're welcome.  I would not be presenting the results to referees, PhD
> examiners or colleagues.
>
>
> http://judgestarling.tumblr.com/post/79974811093/shaming-reputations-as-a-means-of-reducing-the
>
> Happy reading!
>
> F
>
>
> On 30 Oct 2014, at 16:02, Roberto Oliveira Santos <roberto at geodev.com.br>
> wrote:
>
> > Dear Federico
> >
> > Many thanks. Very kind of you the "It would also be completely and
> utterly idiotic.".
> >
> > Best wishes
> >
> > Roberto
> >
> >
> > 2014-10-30 15:56 GMT+00:00 Federico Calboli <f.calboli at imperial.ac.uk>:
> > On 30 Oct 2014, at 15:40, Roberto Oliveira Santos <roberto at geodev.com.br>
> wrote:
> >
> > > Dear all
> > >
> > > Is it possible to run find.clusters without the PCA analysis?
> >
> > I would not know whether find.clusters would like it, but in general you
> can surely find clusters without bothering with a PCA first -- you have a
> formula, you input some data, you get your results.
> >
> > It would also be completely and utterly idiotic.
> >
> > You use a PCA before because of correlation betwen the data, and you
> transform the data with a PCA in a set of independent variables (and you
> also have an idea of what linear combinations explain little or nothing in
> the bargain).  You use a PCA to get some signal out of the noise.
> >
> > So, you can well not use a PCA and cluster.  You will get some results,
> that might, or not, look like the results you get after a PCA
> decomposition.  You will also have biased your clustering to an unknown
> amount, in a way that is not clear what might actually mean.
> >
> > BW
> >
> > F
> >
> >
> > > I have interested in the clustering procedure but would like to
> compare the results with and without PCA transformation.
> > >
> > > Best wishes
> > >
> > > Roberto
> > > _______________________________________________
> > > adegenet-forum mailing list
> > > adegenet-forum at lists.r-forge.r-project.org
> > >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
> >
> >
>
>
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