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

[Ella Bowles]

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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