<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><div><div>Dear Thibaut</div><div>As you know I am new to R. I may need your help and guidance in between.</div><div>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".</div><div><br></div><div>R code starts</div><div><b>> him <- read.csv("him.csv" , header=TRUE)</b></div><div><b>> him</b></div><div><b> 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")</b></div><div><b>> row.names(him)</b></div><div><b>> prcomp(him , scale=TRUE)</b></div><div><b>> plot(prcomp(him))</b></div><div><b>> summary(prcomp(him, Scale=TRUE))</b></div><div><b>>
biplot(prcomp(him , scale=TRUE))</b></div><div><b>> plot(him)</b></div><div>End of R code</div><div><br></div><div>As a result I got a PCA plot (attachment 1), bit similar to PCA done using SPSS.</div><div><br></div><div>NOW I want to know :</div><div> 1) whether I am travelling in the right direction in R.</div><div> 2) if so how to remove the "RED ARROWS" in the Biplot which start from the center and diverge to all directions.</div><div> 3) How to include a symbol in the Biplot and color it.</div><div>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.</div><div>Thank you</div><div>Sincerely</div><div>Arun</div></div></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr
size="1"><b><span style="font-weight: bold;">From:</span></b> "Jombart, Thibaut" <t.jombart@imperial.ac.uk><br><b><span style="font-weight: bold;">To:</span></b> Arun V.S. <vsarun80@yahoo.com><br><b><span style="font-weight: bold;">Sent:</span></b> Fri, March 19, 2010 6:57:20 PM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: Arun<br></font><br>
Dear Arun, <br><br>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:<br><span><a target="_blank" href="http://adegenet.r-forge.r-project.org/">http://adegenet.r-forge.r-project.org/</a></span><br><br>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.<br><br>Best<br><br>Thibaut<br>--<br>######################################<br>Dr Thibaut JOMBART<br>MRC Centre for Outbreak Analysis and Modelling<br>Department of Infectious Disease Epidemiology<br>Imperial College - Faculty of Medicine<br>St Mary’s Campus<br>Norfolk Place<br>London W2 1PG<br>United Kingdom<br>Tel. : 0044 (0)20 7594
3658<br><a ymailto="mailto:t.jombart@imperial.ac.uk" href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><br><span><a target="_blank" href="http://sites.google.com/site/thibautjombart/">http://sites.google.com/site/thibautjombart/</a></span><br><a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a><br><br>________________________________________<br>From: Arun V.S. [<a ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a>]<br>Sent: 19 March 2010 11:47<br>To: Jombart, Thibaut<br>Subject: Arun<br><br>Dear Thibaut<br>Thanks a lot.<br>can I contact you if I need any help in analysing my data.<br>sincerely<br>Arun<br><br><br>________________________________<br>From: "Jombart, Thibaut" <<a ymailto="mailto:t.jombart@imperial.ac.uk" href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>To: Arun V.S. <<a
ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a>><br>Sent: Thu, March 18, 2010 8:13:41 PM<br>Subject: RE: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun<br><br>Dear Arun,<br><br>Thanks for your interest. Here is the pdf of the paper.<br><br>Best regards,<br><br>Thibaut.<br><br><br>--<br>######################################<br>Dr Thibaut JOMBART<br>MRC Centre for Outbreak Analysis and Modelling<br>Department of Infectious Disease Epidemiology<br>Imperial College - Faculty of Medicine<br>St Mary’s Campus<br>Norfolk Place<br>London W2 1PG<br>United Kingdom<br>Tel. : 0044 (0)20 7594 3658<br><a ymailto="mailto:t.jombart@imperial.ac.uk" href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a ymailto="mailto:t.jombart@imperial.ac.uk" href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br><a
href="http://sites.google.com/site/thibautjombart/" target="_blank">http://sites.google.com/site/thibautjombart/</a><br><a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a><br><br>________________________________________<br>From: Arun V.S. [<a ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a><mailto:<a ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a>>]<br>Sent: 18 March 2010 13:24<br>To: Jombart, Thibaut<br>Cc: <a ymailto="mailto:jombart@biomserv.univ-lyon1.fr" href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a><mailto:<a ymailto="mailto:jombart@biomserv.univ-lyon1.fr" href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a>><br>Subject: Fw: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun<br><br>Dear Jambart<br>Please send me
the PDf version of your paper mentioned below<br> Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130; published online 21 January 2009<br>Genetic markers in the playground of multivariate analysis<br>Arun<br><br><br>----- Forwarded Message ----<br>From: Arun V.S. <<a ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a><mailto:<a ymailto="mailto:vsarun80@yahoo.com" href="mailto:vsarun80@yahoo.com">vsarun80@yahoo.com</a>>><br>To: <a ymailto="mailto:jombart@biomserv.univ-lyon1.fr" href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a><mailto:<a ymailto="mailto:jombart@biomserv.univ-lyon1.fr" href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a>>; <a ymailto="mailto:jombart@biomserv.univ-lyon1.fr" href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a><mailto:<a ymailto="mailto:jombart@biomserv.univ-lyon1.fr"
href="mailto:jombart@biomserv.univ-lyon1.fr">jombart@biomserv.univ-lyon1.fr</a>><br>Sent: Mon, March 15, 2010 7:22:51 PM<br>Subject: Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130 REQUEST from Arun<br><br>Dear Jombart<br>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.<br><br><br> Heredity (2009) 102, 330–341; doi:10.1038/hdy.2008.130; published online 21 January 2009<br>Genetic markers in the playground of multivariate analysis<br><br>Best,<br>Arun<br><br><br><br></div></div><div style="position:fixed"></div>
</div><br>
</body></html>