[adegenet-forum] ?==?utf-8?q? Warning message when performing PCA analysis using adegenet package
thomas.hainaux at unamur.be
Mon Apr 3 10:16:23 CEST 2017
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?
> 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
> 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
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