[adegenet-forum] find.clusters without PCA

[Federico Calboli]

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
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> 
>