[adegenet-forum] help with scaleGEN

Danica Fabrigar danica_714 at hotmail.com
Wed Sep 18 12:03:30 CEST 2013

Hi adegenet users,
I am having some trouble interpreting how scaleGEN is supposed to be used when plotting a PCA.
I get very different results when running the following two commands (note: "scale=FALSE" is omitted in the second object):
obj <- scaleGen(mosquitoind, scale=FALSE, missing="mean")
pca.obj <- dudi.pca(obj,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3) 
obj 2<- scaleGen(mosquitoind, missing="mean")
pca.obj2 <- dudi.pca(obj2,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3) 
I guess my question is, what is the appropriate way of using scaleGEN if I want to scale my missing data to the mean allele frequency?
Thanks in advance,
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