[adegenet-forum] PCA issue

[Carlo Pecoraro]

Sorry I wanted to say individuals instead of loci..sorry for the confusion
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Da: Carlo Pecoraro
Inviato: martedì 27 ottobre 2015 16.36
A: adegenet-forum at lists.r-forge.r-project.org
Cc: Jombart, Thibaut
Oggetto: PCA issue

Hi Thibaut and all,

I was trying to visualize what kind of genetic structure I can obtain with my data using the DAPC analysis. I have already filtered the dataset (i.e. missing data, MAF etc) but I have realized there are some loci with a strange deviation from the others that could affect the results of the DAPC. These strange distribution of those loci is clearer underlined doing a PCA. Is there a way to know the name of these loci in order to investigate deeply about them or in case to filter them out?

Many thanks in advance.
Best,
Carlo

--

Carlo Pecoraro, PhD Candidate

Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM)
Dept. Biological, Geological & Environmental Sciences (BiGeA)
University of Bologna
Via S. Alberto 163, 48123 Ravenna (Italy)

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