[R-sig-genetics] genetic analysis SNP

[Jombart, Thibaut]

Hi there, 

this question belongs more to the adegenet forum. 

Here, the error is that you are asking the function to cluster 25 individuals into 40 groups.

Cheers
Thibaut

==============================
Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
Twitter: @thibautjombart



________________________________________
From: R-sig-genetics [r-sig-genetics-bounces at r-project.org] on behalf of karine henry [karine.bounan at florimond-desprez.fr]
Sent: 26 August 2015 11:27
To: r-sig-genetics at r-project.org
Subject: [R-sig-genetics] genetic analysis SNP

Dear all,


I'm trying to use adegenet to analyse a set of 25 lines with 540.000 markers. For the moment, I tried to use genind object as I found file format for SNP genlight object a bit difficult to create.

Everything is going well except when running
grp=find.clusters(obj, max.n.clust=40)
I get graph with cumulative variance and number of retained PC's, but whatever the number of PC I chose I get same error:
number of cluster centers must lie between 1 and nrow(x)

Any idea? Shall it be due to number of markers?

Thanks for your help

regards

Karine

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