[adegenet-forum] Warning message when performing PCA analysis using adegenet package

[Roman Luštrik]

Can you post a small, reproducible example (http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) which we can look at?

Cheers,
Roman

----
In god we trust, all others bring data.

----- Original Message -----
From: "Thomas HAINAUX" <thomas.hainaux at unamur.be>
To: "Roman Luštrik" <roman.lustrik at biolitika.si>
Cc: adegenet-forum at r-forge.wu-wien.ac.at
Sent: Monday, April 3, 2017 10:16:23 AM
Subject: Re: [adegenet-forum] Warning message when  performing PCA analysis using adegenet package

Not really, but i removed the spaces and it didn't change anything.

Le Lundi 3 Avril 2017 09:57 CEST, Roman Luštrik <roman.lustrik at biolitika.si> a écrit:

> Are the spaces around NA (NA.char = " NA ") intended?
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ----- Original Message -----
> From: "Thomas HAINAUX" <thomas.hainaux at unamur.be>
> To: adegenet-forum at r-forge.wu-wien.ac.at
> Sent: Monday, April 3, 2017 9:47:38 AM
> Subject: [adegenet-forum] Warning message when performing PCA analysis using	adegenet package
>
> Hi,
>
> I was performing an PCA analysis on a data set containing  4709 SNPs in
> 144 individuals but I encountered some warning messages that i didn't understood.
> I followed the instructions from the tutorial "An introduction to adegenet 2.0.0" (July 29, 2015).
>
>
> 1) I opened my data and converted it to an genind  object and i got this warning message:
>
> > datacsv = read.csv2("170329_solcap_select_20_98_grouped_by_k3.csv ", header=TRUE)
> > datagenind = df2genind(datacsv[,2:4709], sep= " | ", NA.char=  " NA ")
> Warning message:
> In df2genind(datacsv[, 2:4709], sep = " | ", NA.char = " NA ") :
>   entirely non-type marker(s) deleted
>
> 2) Then I wanted to run the scalegen function and i got a second warning message.
> > datasc = scaleGen(datagenind[,2:4709], NA.method= "mean")
> Warning message:
> In .local(x, ...) : Some scaling values are null.
>  Corresponding alleles are removed.
>
> After running the scalegen function, the number of loci went from 4709 to 3694.
> Why these loci are being removed? Is it possible to keep these value?
>
>
> Thank you very much beforehand for your help and your time.
> I apologise if my questions might be trivial for you, I just started using R recently and i'm not an expert yet.
>
>
> Best regards
> Thomas Hainaux - Researcher
> URBV - Plant Biotechnology
> Namur University
> Rue de Bruxelles 61 - 5000 Namur
> Belgique
>
>
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