[adegenet-forum] Principal coordinate analysis

[Jombart, Thibaut]

Dear Ana Rita, 

this error comes from missing data in the frequency table, which are not handled by dudi.pco. To fix this, you can tell scaleGen to replace missing data, by typing:
obj.X <- scaleGen(obj, center=TRUE, scale=TRUE, method="binom", miss="mean")

Best regards

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 Ana Rita Amaral [aramaral at fc.ul.pt]
Sent: 09 November 2010 17:50
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Principal coordinate analysis

Hi,

I am trying to do a PCA on microsatellite allelic frequencies from a genepop
file. I had no problem creating a geneind object.
I am also able to crate the table itself, which I have named obj.X, using
the command scaleGen(obj, center=TRUE, scale=TRUE, method="binom") but when
I try to do a PCA with that table, I get this error:

dudi.pca(obj.X, center=TRUE, scale=TRUe)
Error in dudi.pca(obj.X, center = TRUE, scale = TRUe) :
  na entries in table

I am not very familiar with R and this is beyond my comprehension! I think
there might be a problem in the table itself, but I cannot see where.
Any help would be appreciated,
Kind regards,

Ana Rita Amaral


-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-
Ana Rita Amaral
Present address:
Centro de Biologia Ambiental
Departamento de Biologia Animal
Faculdade de Ciências Universidade de Lisboa
Campo Grande 1749-016 Lisboa
Portugal
Tel:(+351)21 750 00 00 Ext. 22312
E-mail: aramaral at fc.ul.pt
Web page:http://cba.fc.ul.pt/members/ana_amaral.php

Molecular Ecology Lab
Department of Biological Sciences
Macquarie University
NSW 2109 Australia
-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-





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