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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I’ve already asked the question a week ago, but I’ll just try again, so here we go:</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Dear everybody,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am currently using the adegenet package to perform a structure analysis of my microsatellite dataset and compare it to the results of an analysis using STRUCTURE software. The organism I am working on is an apomictic
plant and I am aware that STRUCTURE is probably not adequate because it assumes HWE and asexuality violates HWE. Nevertheless we use STRUCTURE analysis for apomicts, because in most of the cases the assigned number of groups correlate to biological traits.
Knowing that there is a bias using STRUCTURE we decided to perform a DAPC additionally.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">But now I ran into another problem using adegenet. I am working with a mixed ploidy system with ploidies ranging from 4 to 11. To implement the data into the adgenet package we coded all individuals as 11x because otherwise
it was not possible to load the data. Now I am wondering how big is the bias if the calculation assumes that for example a tetraploid is now a hendecaploid and if I could still trust the results. I am asking because the results of the DAPC are completely different
to the ones of STRUCTURE which puzzles me a bit because I somehow at least expected correlations (the number of optimal k is the same, but the assigned individuals to the clusters differ completely).
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I would appreciate some help<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Stefanie Hilpert<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE">------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE">Stefanie Hilpert<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE">-PhD Candidate-<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-fareast-language:DE">Dept. of Cytogenetics and Genome Analysis<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-fareast-language:DE">Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-fareast-language:DE">Corrensstraße 3, D-06466 Gatersleben Germany<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE">+49 (0)39482 5673<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-fareast-language:DE">IPK Graduate School<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;mso-fareast-language:DE">International Max-Planck Research School<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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