[adegenet-forum] PCA issue

Carlo Pecoraro carlo.pecoraro2 at unibo.it
Tue Oct 27 19:13:21 CET 2015

Sorry I wanted to say individuals instead of loci..sorry for the confusion
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.


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)

IRD (Institut de Recherche pour le Développement)
UMR 212 EME (Ecosytèmes Marins Exploités)
BP 570
Victoria, Mahé

Ph: +39 3337603101
skype contact: carlo_pecoraro

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