<div dir="ltr">Hi Sela<div><br></div><div>For question A: the analyses need not agree - cf figure 1 of the DAPC paper:</div><div><a href="https://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-11-94">https://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-11-94</a><br></div><div><br></div><div>This is because PCA and DAPC maximise different criteria (total variance /vs/ (var between / total var)).</div><div><br></div><div>For question B: in very 'rectangular' data (large p, small n), one can easily find a combination of alleles providing perfect discrimination. I would recommend using cross validation to make sure you don't select too many PCA axes in the DAPC. You will likely find that the less axes you retain in the analyses, the more scatter individuals are. If they remain at the same locations, this likely indicates identical genotypes. </div><div><br></div><div>Best</div><div>Thibaut </div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br>Head of RECON: <a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a><br>WHO Consultant - outbreak analysis</div><div><a href="https://thibautjombart.netlify.com" target="_blank">https://thibautjombart.netlify.com</a><br>Twitter: @TeebzR<br>+44(0)20 7594 3658</div></div></div></div>
<br><div class="gmail_quote">On 26 May 2018 at 20:39, Hanan Sela <span dir="ltr"><<a href="mailto:hans@post.tau.ac.il" target="_blank">hans@post.tau.ac.il</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:courier new,monospace">Hello</div><div class="gmail_default" style="font-family:courier new,monospace">I am trying to study the genetic diversity of a collection of a wheat wild relative. I have a matrix of 105 individuals and ~10000 SNP. Each individual is assigned to a collection site (population). I have done several analyses to investigate the genetic diversity and how it is distributed geographically.</div><div class="gmail_default" style="font-family:courier new,monospace">1. dudi.pca followed by s.class of dudi.pca$li using the population origin as the classing factor.</div><div class="gmail_default" style="font-family:courier new,monospace">2. dapc using the population origin as the grouping factor.</div><div class="gmail_default" style="font-family:courier new,monospace">3. dapc using the grouping results of find.clusters.</div><div class="gmail_default" style="font-family:courier new,monospace"><br></div><div class="gmail_default" style="font-family:courier new,monospace">I have two problems:<br></div><div class="gmail_default" style="font-family:courier new,monospace"><br></div><div class="gmail_default" style="font-family:courier new,monospace">A. The centers of the populations of s.calss from analysis 1 do not agree with the centers of dapc analysis 2 Meaning that some population centers that are one near the other in analysis 1 are very distant one from the other in analysis 2 while the grouping of find.clusters is similar to the plotting of dudi.pca and s.class. <br></div><div class="gmail_default" style="font-family:courier new,monospace"><br></div><div class="gmail_default" style="font-family:courier new,monospace">B. In bouth dpac analyses all of individulas of each group have the excat same coordiates. <br></div><div class="gmail_default" style="font-family:courier new,monospace"><br></div><div class="gmail_default" style="font-family:courier new,monospace">Please help with interpetation of the results. Which analysis represents better the true genetic distances between populations?</div><div class="gmail_default" style="font-family:courier new,monospace"><br></div><div class="gmail_default" style="font-family:courier new,monospace">Thank you <br></div><div class="gmail_extra"><br clear="all"><div><div class="m_3904101932345977654gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Hanan Sela Ph.D.</div>
<div>Curator of the Lieberman Cereal Seed Bank</div>
<div>The Institute for Cereal Crops Improvement<br>Tel-Aviv University</div>
<div>P.O. Box 39040</div>
<div>Tel Aviv 6139001</div>
<div>Israel </div> <div><a href="mailto:hans@tauex.tau.ac.il" target="_blank">E: hans@tauex.tau.ac.il</a> <br></div>
<div>P: <a value="+97236405773">972-3-6405773</a></div>
<div>M: <a value="+972505727458">972-50-5727458</a> <br>F: <a value="+97236407857">972-3-6407857</a></div></div></div></div></div></div></div></div>
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