[adegenet-forum] PCA using R

[Arun V.S.]

Dear Thibaut
As you know I am new to R. I may need your help and guidance in between.
while reading the R manual, I prepared an example "CSV file" file similar to my data. I used the following script to do Principal component analysis using "prcomp".

R code starts
> him <- read.csv("him.csv" , header=TRUE)
> him
 row.names(him) <- c("Chn","Dom","Tib","Bod","Gad","Raj","Mal","Gdb","Guj","GdR","Dgr","Pur","Zan","BrB","BrI","Bal","DgB","DaM","GaB","GjM","Chm")
> row.names(him)
> prcomp(him , scale=TRUE)
> plot(prcomp(him))
> summary(prcomp(him, Scale=TRUE))
> biplot(prcomp(him , scale=TRUE))
> plot(him)
End of R code

As a result I got a PCA plot  (attachment 1),  bit similar to PCA done using SPSS.

NOW I want to know :
 1) whether I am travelling in the right direction in R.
 2) if so how to remove the "RED ARROWS" in the Biplot which start from the center and diverge to all directions.
 3) How to include a symbol in the Biplot  and color it.
When compared to other softwares I think R  simple and suitable for my data. I know it will be quite difficult in the begining but I want to learn it. Please help.
Thank you
Sincerely
Arun

________________________________
From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
To: Arun V.S. <vsarun80 at yahoo.com>
Sent: Fri, March 19, 2010 6:57:20 PM
Subject: RE: Arun

Dear Arun, 

there are two ways you can contact me. First is via the adegenet forum, which is a public mailing list, for general questions about adegenet and genetic data analysis in R. See contact section at:
http://adegenet.r-forge.r-project.org/

The other way is directly via my email. I really encourage using the adegenet forum, since it makes answers available to other users. But for very specific questions, like involving your data or your results (things you don't want to make public), you can contact me directly.

Best

Thibaut
--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: Arun V.S. [vsarun80 at yahoo.com]
Sent: 19 March 2010 11:47
To: Jombart, Thibaut
Subject: Arun

Dear Thibaut
Thanks a lot.
can I contact you if I need any help in analysing my data.
sincerely
Arun


________________________________
From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
To: Arun V.S. <vsarun80 at yahoo.com>
Sent: Thu, March 18, 2010 8:13:41 PM
Subject: RE: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun

Dear Arun,

Thanks for your interest. Here is the pdf of the paper.

Best regards,

Thibaut.


--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: Arun V.S. [vsarun80 at yahoo.com<mailto:vsarun80 at yahoo.com>]
Sent: 18 March 2010 13:24
To: Jombart, Thibaut
Cc: jombart at biomserv.univ-lyon1.fr<mailto:jombart at biomserv.univ-lyon1.fr>
Subject: Fw: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun

Dear Jambart
Please send me the PDf version of your paper mentioned below
  Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130; published online 21 January 2009
Genetic markers in the playground of multivariate analysis
Arun


----- Forwarded Message ----
From: Arun V.S. <vsarun80 at yahoo.com<mailto:vsarun80 at yahoo.com>>
To: jombart at biomserv.univ-lyon1.fr<mailto:jombart at biomserv.univ-lyon1.fr>; jombart at biomserv.univ-lyon1.fr<mailto:jombart at biomserv.univ-lyon1.fr>
Sent: Mon, March 15, 2010 7:22:51 PM
Subject: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun

Dear Jombart
I would like to introduce myself as Mr V.S.Arun, doing my research on Human migration and evolution -India. After working for three years in the lab (YSNP - Taqman: YSTR - Fragment analysis), its time for me to start analyzing all the data I have. I am using R for analyzing my data (Beginner - trying to use R) . I would like to read your paper mentioned below. Please send me the same as PDF. It will be of great help to me.


  Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130; published online 21 January 2009
Genetic markers in the playground of multivariate analysis

Best,
Arun


      
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