[adegenet-forum] more clusters with less PCs retained in find.clusters
lucia.maffey at gmail.com
Sun May 12 19:00:24 CEST 2019
I'm performing DAPC analyses on radseq data from mosquitoes. When I run the
previous find.clusters function, I get larger K values (that is more
clusters) when I retain fewer PCs. For example, I have a data set of 40
individuals (with over 80.000 SNPS). When I retain 30-38 PCs, I get K=1 and
when I choose to retain 15 PCs, I get K=3. Shouldn't it be the other way
around? More PCs retained smaller K and vicecersa? When I run the same data
in Structure I get K=3 so I tend to think that I should retain fewer PCs
in find.clusters but as the vignette explains that you should retain all of
them, I'm worried I'm missing something here. I've been searching the
archive but only found the same question unanswered.
Thanks in advance!!!
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