[adegenet-forum] find.clusters producing different 'best' solutions in different runs

[Pip Griffin]

Dear Thibaut and Adegenet users,

I have a polyploid dataset coded as binary (PA datatype) containing 297
individuals and 97 'loci' (microsatellite alleles). I've been implementing
the find.clusters command, retaining 40 PCA axes to capture >95% of the
variance.

The issue is that I get different 'best' solutions for the number of K
clusters in different find.clusters runs, with a modal value of 9, but
ranging from 6-12.  Obviously the actual differences in BIC value are pretty
small, but even when I designate a 'cut-off' (e.g. when the BIC value must
decrease by at least 2 for the solution to be 'better' than the previous K),
there is variation in the solution.

This variability is even higher when I choose fewer PCA axes to retain (e.g.
retaining 80% of the variance), as would be expected, but even when I use
100 PCA axes (>>95% of variance), the value varies between 'runs'.

Has anyone else observed this - and do you have any advice?

Thanks for your help

Pip
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