[adegenet-forum] help with scaleGEN

[Danica Fabrigar]

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):
 
A)
obj <- scaleGen(mosquitoind, scale=FALSE, missing="mean")
pca.obj <- dudi.pca(obj,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3) 
 
B)
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,
Danica
 		 	   		  
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