[adegenet-forum] number of alleles using microsatellite data for polyploids

[Jombart, Thibaut]

Hello, 

I am sorry but I am not sure I understand the problem. hexaploid data are OK as long as all individuals have the same ploidy. For the rest you can import the data using df2genind, and all should run smoothly. 

If I'm missing the point, please post a (reproducible) example, showing what's wrong.

Best
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: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Maria del Carmen David [maria.david.salas at gmail.com]
Sent: 25 August 2014 22:20
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] number of alleles using microsatellite data for       polyploids

Hello,
I have a microsatellite data set of an hexaploid organism. I have uploaded the data but when I call for the number of alleles per locus I get an extra allele (0), it is cause for the zeros I have to put so the data can make sense. Now, I'm worried that this allele frequency will distortion my results because I want to make a DAPC. In the package "poppr" there's a command called "recode.polyploids" to eliminate that extra allele but after reading adegenet tutorials I haven't found any comment about this issue. Should I eliminate this extra allele or leave my data as it is? Thank you for your help.

Maria del Carmen David