[adegenet-forum] dealing with colinear variables in dapc

[sophie bouchet]

when removing markers with NULL variance within one of the two main groups,
it works.


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

>
> 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
>
>
>
>
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