<div dir="ltr"><div><div><div>Hi,</div><br></div>DAPC is very sensitive to the number of PC you choose. I suspect what may be happening here is that you have picked exactly the same number of PC in your DAPC as you chose to pick your clusters. This results in a bit of circular logic where you are asking the discriminant function to discriminate your groups based on the exact principal components you used to define your groups. Because of that, the between-group separation is so vast that your within group differences is negligible. <br><br></div><div>Instead, what you should do is use the xvalDapc function to perform a cross-validation to avoid over-fitting.</div><div><br></div><div>Best,<br></div><div>Zhian<br></div><div><div><div><div><br><div class="gmail_quote"><div dir="ltr">On Sun, Oct 28, 2018 at 11:00 AM <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send adegenet-forum mailing list submissions to<br>
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1. dapc (amir naji)<br>
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Date: Fri, 27 Oct 2017 19:44:03 +0330<br>
From: amir naji <<a href="mailto:amnaji1970@yahoo.com" target="_blank">amnaji1970@yahoo.com</a>><br>
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Hi<br>
I read my dart date set using dart R package (62 genotype and 12500 snp loci).<br>
I built a DAPC scatter plot without using a priori grouping information using this command line: dapc <- dapc(data, grp$grp).grp was created by using find.clusters command. But in scatter plot (I used scatter(dapc) command) only three points representing each group were seen and individuals were not shown in scatter plot. I couldn?t find the reason and I hope to got help on that.<br>
Thanks for your help<br>
Amir<br>
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