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

[Ella Bowles]

Thank you Thibaut -- given this, I am guessing that I shouldn't worry about
the warning? It only removed one locus from my file, anyway, when I compare
the dataset loaded in to the "mat" dataset.

With thanks,

On Tue, May 1, 2018 at 1:54 PM, Thibaut Jombart <thibautjombart at gmail.com>
wrote:

> 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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>>
>
>


-- 
Ella Bowles, PhD
Postdoctoral Researcher
Department of Biology
Concordia University

Website: https://ellabowlesphd.wordpress.com/
Email: bowlese at gmail.com
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