[adegenet-forum] how do I know if missing data is affecting PCA or DAPC results

Ella Bowles ebowles at ucalgary.ca
Tue Sep 22 21:16:31 CEST 2015


I'm attempting to do a PCA and a DAPC on genomic data, 186 individuals
spread over 11 putative populations, with just over 4000 loci. I have
converted the data to a genlight object. I'm wondering, I know that I have
some missing data (markers are present in at least 65% of individuals). In
the Adegent manual it specifies that missing data could bias results. How
do I know if I have too much missing data, or should I just get rid of all
the loci that have missing values before doing the analysis?

With thanks,

Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca, bowlese at gmail.com
website: http://ellabowlesphd.wordpress.com/
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