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<p class="MsoNormal">Hello all,</p><p class="MsoNormal"><br></p>
<p class="MsoNormal">I’m new to adegenet and was wondering if I could ask for
some advice.<span style="mso-spacerun:yes"> </span>I’m working with a dataset
of microsatellite markers from a haploid fungus which reproduces both asexually
and sexually (it seems).<span style="mso-spacerun:yes"> </span>Therefore the
dataset has many clones which can be present in many locations.<span style="mso-spacerun:yes"> </span>I am looking to do a sPCA and was wondering
if the clonality in the dataset will influence the sPCA.<span style="mso-spacerun:yes"> </span>I cannot use the clone-corrected dataset
because a single clone can be present in many locations.<span style="mso-spacerun:yes"> </span>Does anyone have any experience of this? Will
a sPCA with many clones still produce reliable results?<span style="mso-spacerun:yes"> </span>I can’t think why not but maybe I’m missing
something.</p><p class="MsoNormal"><br></p>
<p class="MsoNormal">Also, a more technical question. I see a cline with a
distinct group (particularly clear when using colorplot).<span style="mso-spacerun:yes"> </span>Is there any way to draw out the groups from
the sPCA?<span style="mso-spacerun:yes"> </span>I assume it is in the $ls or
$li component of the sPCA output but looking at these the cutoff is nowhere as
clear as on the graphical output.</p><p class="MsoNormal"><br></p>
<p class="MsoNormal">Thank you in advance, and sorry if the questions are too
simplistic.</p><p class="MsoNormal"><br></p>
<p class="MsoNormal">Martin</p>
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