[adegenet-forum] Inconsistent DAPC

[Vojtěch Zeisek]

Hi,
I was running DAPC on almost 500 individuals (over 60 populations) genotyped 
by 10 microsatellite primers as follows:
kfind <- find.clusters(genind, n.pca=100, stat="BIC", choose.n.clust=FALSE, 
criterion="diffNgroup", max.n.clust=75, n.iter=100000000, n.start=10000, 
scale=FALSE, pca.select="nbEig", truenames=TRUE)
table.value(table(pop(genind), kfind$grp), col.lab = paste("kfind", 
1:length(kfind$size)))
dapc <- dapc(genind, kfind$grp, n.pca=35, n.da=20, center=TRUE, scale=FALSE, 
var.contrib=TRUE, pca.info=TRUE, pca.select="nbEig", truenames=TRUE)
scatter(dapc, main="DAPC", posi.da=“bottomleft“)
When I did it for first time, I've got nice partitioning to 3 clusters, quiet 
similar to output of Structure and PCoA. When I tried it second time with same 
parameters, I've got division to 12 groups. So I wonder how is it possible and 
how to trace to make it reproducible and find out why it shifted so much.
Sincerely,
Vojtěch

-- 
Vojtěch Zeisek
http://trapa.cz/en/

Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/

Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic
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