[adegenet-forum] Inconsistent DAPC

Vojtěch Zeisek vojta at trapa.cz
Wed Jul 9 12:34:47 CEST 2014

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$grp), col.lab = paste("kfind", 
dapc <- dapc(genind, kfind$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.

Vojtěch Zeisek

Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ

Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ

Czech Republic
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 490 bytes
Desc: This is a digitally signed message part.
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20140709/b040c91c/attachment.sig>

More information about the adegenet-forum mailing list