[adegenet-forum] find.clusters without PCA

[Roberto Oliveira Santos]

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
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> >
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>
>
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