<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.hps
{mso-style-name:hps;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=FR link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear Dr Jombart, <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>Thank you very much for answering me so fast. <o:p></o:p></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'>Please find attached a part of my data set in csv file : <o:p></o:p></span></span></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width=334 style='width:250.65pt;margin-left:-.75pt;border-collapse:collapse'><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>marker<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>sbPb-3066557<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>sbPb-3066720<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>sbPb-3066853<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta patula <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta patula <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>0<o:p></o:p></span></p></td></tr><tr style='height:12.75pt'><td width=94 nowrap valign=bottom style='width:70.65pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>Beta macrocarpa <o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal align=right style='text-align:right'><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>1<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:12.75pt'><p class=MsoNormal><span style='font-size:10.0pt;color:black;mso-fareast-language:FR'>NA<o:p></o:p></span></p></td></tr></table><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'> I didn’t know how to add the geographical data, so I put them in a second sheet : <o:p></o:p></span></span></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width=160 style='width:120.0pt;margin-left:-.75pt;border-collapse:collapse'><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal><span style='color:black;mso-fareast-language:FR'>x<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal><span style='color:black;mso-fareast-language:FR'>y<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>33.3333<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>34.7333<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>33.6167<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>34.8<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>27.202148<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>35.532226<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>27.202148<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>35.532226<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>19.599609<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>47.115<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>34.4667<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>31.4167<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>34.4667<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>31.4167<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>-7.76667<o:p></o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'>37.0667<o:p></o:p></span></p></td></tr><tr style='height:15.0pt'><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:black;mso-fareast-language:FR'><o:p> </o:p></span></p></td><td width=80 nowrap valign=bottom style='width:60.0pt;padding:0cm 3.5pt 0cm 3.5pt;height:15.0pt'><p class=MsoNormal align=right style='text-align:right'><span style='color:black;mso-fareast-language:FR'><o:p> </o:p></span></p></td></tr></table><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'>The name of my data set in R is : “test”. So I first try to convert my data set into genind object with this script of genind constructor : <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>test <- <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> read.table("//Serveur/m/13 - STAGIAIRES BETTERAVES/2012_tyfanie BOURLET/AKER/sPCA/testspca.txt",<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>test <- sqlQuery(channel = 3, select * from [test sPCA$])<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>names(test) <- make.names(names(test))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>x <- as.matrix(test)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>genind(test,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>as.genind(test,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>is.genind(test)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'>And R put me this : <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> test <- <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>+ read.table("//Serveur/m/13 - STAGIAIRES BETTERAVES/2012_tyfanie BOURLET/AKER/sPCA/testspca.txt",<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>+ header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> test <- sqlQuery(channel = 3, select * from [test sPCA$])<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> names(test) <- make.names(names(test))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> x <- as.matrix(test)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> genind(test,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> #####################<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> ### Genind object ### <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> #####################<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>- genotypes of individuals - <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>S4 class: genind<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@call: genind(tab = test, pop = NULL, prevcall = NULL, ploidy = 2, type = c("codom", <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> "PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@tab: 1114 x 255 matrix of genotypes<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@ind.names: vector of 1114 individual names<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.names: vector of 2 locus names<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.nall: number of alleles per locus<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.fac: locus factor for the 255 columns of @tab<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@all.names: list of 2 components yielding allele names for each locus<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@ploidy: 2<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@type: codom<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>Optionnal contents: <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@pop: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@pop.names: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@other: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> as.genind(test,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> #####################<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> ### Genind object ### <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> #####################<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>- genotypes of individuals - <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>S4 class: genind<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@call: as.genind(tab = test, pop = NULL, prevcall = NULL, ploidy = 2, <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> type = c("codom", "PA"))<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@tab: 1114 x 255 matrix of genotypes<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@ind.names: vector of 1114 individual names<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.names: vector of 2 locus names<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.nall: number of alleles per locus<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@loc.fac: locus factor for the 255 columns of @tab<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@all.names: list of 2 components yielding allele names for each locus<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@ploidy: 2<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@type: codom<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>Optionnal contents: <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@pop: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@pop.names: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>@other: - empty -<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>> is.genind(test)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>[1] FALSE<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'>So apparently R doesn’t consider that my data set is a genind object…<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'>And then when I want to start the sPCA analysis I enter this script : <o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>library(adegenet)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>library(adehabitat)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>data(test)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>obj <- test$dat2A<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>obj<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>test <- test$dat2A<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>test<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>head(truenames(obj[loc="sbPb"])$tab)<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN>And R put me this : <span style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> WARNING: Warning in data(test) : data set 'test' not found<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'> ERROR:<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#558ED5;mso-style-textfill-fill-color:#558ED5;mso-style-textfill-fill-alpha:100.0%'>error in evaluating the argument 'x' in selecting a method for function 'truenames'<o:p></o:p></span></span></p><p class=MsoNormal><span class=hps><span lang=EN style='color:#222222'><o:p> </o:p></span></span></p><p class=MsoNormal><span lang=EN>And I have another problem. When I import my data set in csv format, R take only the 255 first columns (I have 4630 columns) so I have to import my data in text format but then, R give me this error message : “[10] ERROR: line 16 did not have 4631 elements” whereas all my lines have 4630 elements…<o:p></o:p></span></p><p class=MsoNormal><span lang=EN><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN>Thanking you in advance for helping me. I’m not an expert at all with R but it would be very helpful if I can manage this sPCA.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN>Best regards, <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:FR'>Tyfanie Bourlet<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>France<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>Florimond Desprez<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>Beet laboratory<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>Student at Agrocampus Ouest<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>0672610237<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>