[adegenet-forum] find.clusters without PCA

Federico Calboli f.calboli at imperial.ac.uk
Thu Oct 30 16:56:34 CET 2014

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.



> 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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