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<body class='hmmessage'><div dir='ltr'>Hi Thibaut,<div><br></div><div>Thank you for the clarification. I got confused myself there.</div><div><br></div><div>What you've said made a lot of sense, are there cases in genetics in which scaling would be a good idea?</div><div><br></div><div><br></div><div>Regards,</div><div>Danica</div><div><br></div><div><br><br> ________________________________________<br><div>> From: t.jombart@imperial.ac.uk<br>> To: danica_714@hotmail.com; adegenet-forum@lists.r-forge.r-project.org<br>> Subject: RE: [adegenet-forum] help with scaleGEN<br>> Date: Wed, 18 Sep 2013 14:53:53 +0000<br>> <br>> Hello, <br>> <br>> I think some clarification should help here.<br>> <br>> "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.<br>> <br>> 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).<br>> <br>> Best<br>> Thibaut<br>> <br>> <br>> ________________________________________<br>> From: adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Danica Fabrigar [danica_714@hotmail.com]<br>> Sent: 18 September 2013 11:03<br>> To: adegenet-forum@lists.r-forge.r-project.org<br>> Subject: [adegenet-forum] help with scaleGEN<br>> <br>> 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></div> </div></body>
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