[adegenet-forum] question on scaleGen()

[Thibaut Jombart]

Hello,

sorry, I am not sure I understand: what is the problem?

Cheers
Thibaut

--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR


On 25 November 2016 at 15:23, Da Pan <panda143526 at gmail.com> wrote:
> Dear Thimbaut and adegenet users,
> Thank you for your time and help.
> I probably have some more naif questions about adegenet.
> I am attemping a PCA analysis on my SNP dataset with the following
> arguements:
>
> test <- read.structure("batch_1.str",n.ind = 17, n.loc =  12451, col.lab =
> 1, col.pop = 2, row.marknames = 1, NA.char = "0")
>
> test2 <- scaleGen(test, NA.method = "mean")
>
> After this, the R shows:
>
> Warning message:
> In .local(x, ...) : Some scaling values are null.
>  Corresponding alleles are removed.
>
> I checked pop(test), it returned as :
>
>  1  3  5  7  9 11 13 15 17 19 21 23 25 27 29 31 33
> 02 02 04 04 06 06 07 07 19 19 38 38 39 39 46 46 46
> Levels: 02 04 06 07 19 38 39 46
>
> How to solve this problem?
>
> thanks in advance
>
> Best wishes,
> Da
>
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