[adegenet-forum] spatial pca with large SNP data

[anne DaSilva]

Dear all,
I would like to conduct a spatial PCA with 24000 SNP (after pruning). If I understand spca is not possible with a genlight object, so I use PLINK to recode my data in a STRUCTURE format, and then I work on a genind object in R....but the analysis ends....because of the size of the genind object I imagine.
Is there a solution (split the data? but how?)?
I am loosing all my hair over that problem (perhaps pathetically simple....)  and I would be really grateful if someone could help me to escape from my ignorance....
Kind regards
Anne



 Anne Blondeau Da Silva
 Unité de Génétique Moléculaire Animale
 UMR 1061 INRA-Université de Limoges
 Faculté des Sciences et Techniques
 123 Avenue Albert Thomas
 87060 LIMOGES Cedex
 Tél. 05 55 45 76 75
 Fax. 05 55 45 76 53
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