[adegenet-forum] help with scaleGEN

[Jombart, Thibaut]

Hello, 

I think some clarification should help here.

"scaling" means transforming a variable to that its variance is 1. It is usually used to remove the effects of variances inherently different across a bunch of variables (typically because of different units). In genetics, most of the time, I think scaling is a bad idea: all variable have the same unit, and differences in variances are probably meaningful.

missing="mean" refers to the procedure for replacing missing data. They are set to the origin, which is the mean of the corresponding allele frequencies (typically the 'non-informative' point in PCA).

Best
Thibaut


________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Danica Fabrigar [danica_714 at hotmail.com]
Sent: 18 September 2013 11:03
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] help with scaleGEN

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