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

[Thibaut Jombart]

Indeed, you should be able to ignore this, unless you know all sites were
polymorphic.

Best

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 19:53, Ella Bowles <bowlese at gmail.com> wrote:

> 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
>>>
>>> _______________________________________________
>>> adegenet-forum mailing list
>>> adegenet-forum at lists.r-forge.r-project.org
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>>> /adegenet-forum
>>>
>>
>>
>
>
> --
> Ella Bowles, PhD
> Postdoctoral Researcher
> Department of Biology
> Concordia University
>
> Website: https://ellabowlesphd.wordpress.com/
> Email: bowlese at gmail.com
>
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