[adegenet-forum] needed discussed of error running xval, some scaling values are null

Thibaut Jombart thibautjombart at gmail.com
Tue May 1 19:54:36 CEST 2018


Hi Ella

the function 'tab' now replaces 'scaleGen', but it shouldn't change much.
This warning suggests some loci are fixed, and genind objects only stores
polymorphic sites.

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 1 May 2018 at 18:11, Ella Bowles <bowlese at gmail.com> wrote:

> Hello,
>
> I am getting an error running xval that has already been posted about:
> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2011-May/
> 000282.html
> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2016-November/
> 001510.html
> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2017-April/
> 001579.html
>
> However, as far as I have found, the only response was from the 2011 post,
> and said that group member ship had to be provided. I think I have done
> this. Can you provide any advice on how i can trouble shoot this error to
> figure out if there is something wrong with my file?
>
> Specifically, I am trying to run xval (in prep for DAPC) on a dataset with
> 74 individuals and 7820 loci. Data is attached. I may not be able to run
> DAPC on the dataset, since it is possible that I have no population
> structure here, but that is what I'm trying to see. If do have structure,
> it shouldn't be more than two groups. Anyway, I run the following:
>
> rm(list=ls(all=T))
>
> #load packages
> library("ape")
> library("genetics")
> library("pegas")
> library("seqinr")
> library("ggplot2")
> library("adegenet")
>
> TaNoOdds <- read.structure("TaNoOddsWithOutsFilled.STRU", n.ind = 74,
> n.loc = 7820, onerowperind = FALSE, col.lab = 1, col.pop = 2, col.others =
> NULL, row.marknames = 1, NA.char = "0", ask = TRUE)
>
>  mat <- scaleGen(TaNoOdds, NA.method="mean")
>
> ##then I get this error message
> Warning message:
> In .local(x, ...) : Some scaling values are null.
>  Corresponding alleles are removed.
>
> I have run this exact same set of commands on seven other files  with no
> problem. Any thoughts about how to trouble-shoot are much appreciated.
>
> With thanks,
> Ella
>
> --
> Ella Bowles, PhD
> Postdoctoral Researcher
> Department of Biology
> Concordia University
>
> Website: https://ellabowlesphd.wordpress.com/
> Email: bowlese at gmail.com
>
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