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
genetic analysis SNP
2 messages · karine henry, 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
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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