[adegenet-forum] (no subject)

[Alex BAUMEL]

hi,

I found the problem, it was simply because I insert the ID number in the data, 

it works well now.


thanks

alex baumel 



> ----------------------------------------
> From: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
> Sent: Tue Nov 04 11:59:24 CET 2008
> To: Alex BAUMEL <alex.baumel at univ-cezanne.fr>
> Subject: Re: [adegenet-forum] (no subject)
> 
> 
> Dear Axel,
> > Hi,
> >
> > spca seems to work well on my AFLP data,
> >
> > 3 questions :
> >
> > -  I need to scale (scale =TRUE) the data, and I do not understand the reason.
> >   
> Why do you 'need' to scale? Is there an error otherwise? In any case, 
> scaling may be useful, but it is never mandatory.
> > - Another problem  the function screeplot does not work on my spca object.?
> >   
> What is the error message?
> > - Is it possible to start spca from a  matrix of genetic distance between genotypes ?
> >   
> Not currently, and likely not in a near future. I would have to check if 
> the principle of sPCA is extendable to distances matrices. What may be 
> available sooner would be data transformation so that the Euclidean 
> distances between transformed genotypes would correspond to a given 
> genetic distance between raw genotypes.
> 
> Could you please post a sample dataset that reproduces the error? For 
> instance, if 'obj' is your object, give this a try:
> ##
> samp <- sample(1:nrow(obj),20)
> objToPost <- obj[samp, 1:30]
> ##
> 
> if spatial coordinates are inside obj at other$xy, they should be subsetted 
> at the same time (check objToPost$other$xy).
> 
> Also, we would need to know which version of adegenet you are using 
> (there are changes between the devel and the last stable version).
> 
> Best regards,
> 
> Thibaut.
> 
> 
> > If anyone can help ...
> >
> > Alex Baumel
> >
> > Institut Méditerranéen d'Ecologie et de Paléoécologie
> > Bâtiment Villemin
> > Europole de l'Arbois - BP 80
> > F 13545 Aix-en-Provence cedex 04
> > phone: (33) 442 908 453
> > fax: (33) 442 908 448
> >
> > web page : http://alexbaumel.blogspot.com/
> > _______________________________________________
> > adegenet-forum mailing list
> > adegenet-forum at lists.r-forge.r-project.org
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
> >
> >
> >
> >   
> 
> 
> -- 
> ######################################
> Thibaut JOMBART
> CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
> Universite Lyon 1
> 43 bd du 11 novembre 1918
> 69622 Villeurbanne Cedex
> Tél. : 04.72.43.29.35
> Fax : 04.72.43.13.88
> jombart at biomserv.univ-lyon1.fr
> http://biomserv.univ-lyon1.fr/%7Ejombart/
> http://adegenet.r-forge.r-project.org/