[adegenet-forum] dealing with colinear variables in dapc

[Jombart, Thibaut]

Hello, 

no, I'm afraid there is not. 

If you send a reproducible example someone might figure out what's going on. Sorry, I'm on holiday and won't look again at my computer in a while.

Best
Thibaut
________________________________________
From: bouchet.sophie at gmail.com [bouchet.sophie at gmail.com] on behalf of sophie bouchet [bouchet.sophie at free.fr]
Sent: 31 July 2013 10:42
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] dealing with colinear variables in dapc

Thanks,

I guess this is within group variance? because I reu moved very low maf markers.

Is there any function in adegenet that gives within group variable variance?

Sophie


2013/7/31 Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>
Hello,

collinearity is not the problem here, but variables with NULL variance give undefined F statistics and should this be discarded.

Best
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of sophie bouchet [bouchet.sophie at free.fr<mailto:bouchet.sophie at free.fr>]
Sent: 30 July 2013 17:00
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] dealing with colinear variables in dapc

Dear Thibault,

When running dapc on a dataset containing 174 individuals and 10000 SNP markers, I obtain this error message :

Erreur dans lda.default(x, grouping, ...) :
  variables 1 2 appear to be constant within groups

Do I need to remove colinear markers from the dataset before running dapc?

Thanks,

Sophie