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</o:shapelayout></xml><![endif]--><style type="text/css">.style1 {font-family: "Times New Roman";}</style></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'>Hello,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'>I followed the DAPC tutorial and produced a scatter plot using the following commands<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>> rul<-read.structure("1548SNPsQ60_427_scc30_sec10_nuclear_195ampl.str",missing=-9,quiet=FALSE)<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>> grp <- find.clusters(rul, max.n.clust=10, n.start=200)<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'>Choose the number PCs to retain (>=1): <o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>400<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'>Choose the number of clusters (>=2: <o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>4<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>> dapcgrp1 <- dapc(rul, grp$grp)<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'>Choose the number PCs to retain (>=1): <o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>15<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'>Choose the number discriminant functions to retain (>=1): <o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>3<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-all'><span style='font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-GB'>> scatter(dapcgrp1, scree.da=FALSE, solid=1)</span><span style='font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><img width=637 height=467 id="_x0000_i1029" src="cid:image004.jpg@01D27005.C5EFCC20"></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0053FA'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1631F6;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1631F6;mso-fareast-language:EN-GB'>If I do the same thing without the find.clusters step using the following commands I get quite a different scatter plot<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1631F6;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><pre style='word-break:break-all'><span class=gcg2ujhdabb><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>> </span></span><span class=gcg2ujhdeab><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>dapc1 <- dapc(rul)<o:p></o:p></span></span></pre><pre style='word-break:break-all'><span style='font-family:"Lucida Console";color:black;background:#E1E2E5'>Choose the number PCs to retain (>=1): <o:p></o:p></span></pre><pre style='word-break:break-all'><span class=gcg2ujhdeab><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>15<o:p></o:p></span></span></pre><pre style='word-break:break-all'><span style='font-family:"Lucida Console";color:black;background:#E1E2E5'>Choose the number discriminant functions to retain (>=1): <o:p></o:p></span></pre><pre style='word-break:break-all'><span class=gcg2ujhdeab><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>3<o:p></o:p></span></span></pre><pre style='word-break:break-all'><span class=gcg2ujhdabb><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>> </span></span><span class=gcg2ujhdeab><span style='font-family:"Lucida Console";color:blue;background:#E1E2E5'>scatter(dapc1, scree.da=FALSE, solid=1)</span></span><span style='font-family:"Lucida Console";color:black;background:#E1E2E5'><o:p></o:p></span></pre><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1631F6;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><img width=648 height=476 id="Picture_x0020_3" src="cid:image006.jpg@01D27005.C5EFCC20"></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>Although the two plots look somehow similar, the contents and overlap of the groups is different. For example, none of the samples in ‘Group 2’ (dapc(x, grp$grp)) are in ‘hispanica’ (dapc(x)) – Group 2 and hispanica are the two small outlier groups occupying the ‘same’ space in the two DAPC analyses. Looking at the inferred/original table it’s obvious that with dapc(x, grp$grp) samples in my predefined ‘hispanica’ group are put together with other samples into group 3 (where most of my ‘non-native’ samples fall), whereas with dapc(x) they more or less are in their own group (which makes biological sense). <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><img width=526 height=388 id="Picture_x0020_4" src="cid:image009.jpg@01D27005.C5EFCC20"></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>dapc(x, grp$grp)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><img width=529 height=390 id="Picture_x0020_5" src="cid:image013.jpg@01D27005.C5EFCC20"></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>dapc(x)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>This raises the question why the two analyses of the same data set produce rather different results and which one should ‘believe’? Any help or ideas are appreciated.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>Thank you<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'>Markus<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>Dr Markus Ruhsam<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>Molecular Plant Ecologist<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>Royal Botanic Garden Edinburgh<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>20A Inverleith Row<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>Edinburgh <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>EH3 5LR<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>United Kingdom<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>Tel: +44 (0) 131 248 2859<br>Fax: +44 (0) 131 248 2901 <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'><a href="http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage"><span style='color:#1616F6;text-decoration:none'>http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage</span></a> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#1616F6;mso-fareast-language:EN-GB'>The mission of the Royal Botanic Garden Edinburgh is to “<b>To explore, conserve and explain the world of plants for a better future</b>”<o:p></o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#0070C0;mso-fareast-language:EN-GB'><o:p> </o:p></span></b></p><p class=MsoNormal><span style='color:#0053FA;mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D;mso-fareast-language:EN-GB'><img border=0 width=325 height=105 id="Picture_x0020_2" src="cid:image001.png@01D26FFF.59E41870" alt="cid:image002.png@01D09F78.9DFBA130"></span><span style='color:#0053FA;mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div>
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