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

[Thibaut Jombart]

No probs!

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 <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 10 April 2017 at 13:29, Thomas HAINAUX <thomas.hainaux at unamur.be> wrote:

>  Hi,
>
> you are right, there is no reason to keep this value.
> Sorry for this silly question, i was troubled by the warning messages.
>
>
> Thank you for your help.
>
> Best regards
> Thomas
>
> Le Lundi 3 Avril 2017 10:37 CEST, Thibaut Jombart <
> thibautjombart at gmail.com> a écrit:
>
> > Hi there,
> >
> > this is the expected behaviour when loci are non-polymorphic. Why
> > would you like to keep them? Especially in the context of a PCA, where
> > it will creates variables with a variances of zero, and therefore Inf
> > values when scaling?
> >
> > 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
> > +44(0)20 7594 3658
> >
> >
> > On 3 April 2017 at 09:21, Roman Luštrik <roman.lustrik at biolitika.si>
> wrote:
> > > 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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>
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>
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