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

[Thibaut Jombart]

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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