[adegenet-forum] DAPC

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu May 19 10:51:41 CEST 2011


you may have forgotten to provide group memberships. What does "pop(obj)" return? If it is missing, you need to provide something for the argument "pop". See ?find.clusters to identify clusters without priors.


From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Martin Llewellyn [llewellynmartin at hotmail.com]
Sent: 18 May 2011 16:46
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC

Hi Thimbaut and adegenet users

Thanks for your help on getting the package running. All working now.

I am attempting a DAPC on a genind object containing no missing data with 264 isolates and 24 microsat loci with the arguement:

dapc <- dapc(obj, pop=NULL, n.pca=NULL, n.da=NULL, scale=TRUE,scale.method=c("sigma"), truenames=TRUE, all.contrib=FALSE,pca.select=c("nbEig"), perc.pca=NULL)

Choose the number PCs to retain (>=1): (I put 2 - 15)

Message returned is:-

Error in svd(X, nu = 0) : infinite or missing values in 'x'
In addition: Warning message:
In .local(x, ...) : Some scaling values are null.
Corresponding alleles are removed.

Any advice most appreciated


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