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<body class='hmmessage'><div dir='ltr'>Hi adegenet users,<BR> <BR>I am having some trouble interpreting how scaleGEN is supposed to be used when plotting a PCA.<BR> <BR>I get very different results when running the following two commands (note: "scale=FALSE" is omitted in the second object):<BR> <BR>A)<BR>obj <- scaleGen(mosquitoind, scale=FALSE, missing="mean")<br>pca.obj <- dudi.pca(obj,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3) <BR> <BR>B)<BR>obj 2<- scaleGen(mosquitoind, missing="mean")<br>pca.obj2 <- dudi.pca(obj2,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3) <BR> <BR> <BR>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?<BR> <BR> <BR>Thanks in advance,<BR>Danica<BR> </div></body>
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