[adegenet-forum] Inconsistent DAPC

Vojtěch Zeisek vojta at trapa.cz
Wed Jul 9 16:39:06 CEST 2014

Hello, thank You very much.

Dne St 9. července 2014 10:49:04 jste napsal(a):
> Hello there,
> this is because you are using a fixed criteria to decide the group
> partitioning. This was only designed for simulated data analysis, or cases
> where one needs to analyse hundreds of datasets.
> Best for your to look at the BIC curves (over a couple of iterations) and
> assess which clustering solution you want to retain.

Ah, right. When running it like this
kfind <- find.clusters(genind, max.n.clust=75, stat="BIC", 
choose.n.clust=TRUE, n.iter=100000000, n.start=10000, scale=FALSE, 
table.value(table(pop(genind), kfind$grp), col.lab=paste("Inferred cluster", 
1:length(kfind$size)), grid=TRUE)
I see there are more possible solutions... Interesting data set. :-)

> Best
> 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 Vojtěch
> Zeisek [vojta at trapa.cz] Sent: 09 July 2014 11:34
> To: Adegenet R-Forum
> Subject: [adegenet-forum] Inconsistent DAPC
> 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

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
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