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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi,<o:p></o:p></p><p class=MsoNormal>Introduction:<o:p></o:p></p><p class=MsoNormal>I’m analyzing a high replicate tag based mRNAseq (SAGE like) data set. In the experiment I have 2x 47 replicates of true biological samples of potato leaves. I also have triplicates of libraries originating from the same crushed leaf material, but from different library preps. I hope to be able to evaluate biological and technical variation from these. I have chosen to use EgdeR for the analysis, while it has some very attractive features. One is that it is possible to estimate the dispersion.<o:p></o:p></p><p class=MsoNormal> For now I can conclude that the tagwise dispersion model fits the data better than the poisson and the common dispersion model (not suerpringly).<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Howerver when calculating the tagwise dispersion, prior.n and used.prop needed to be defined. I have looked in the forum and found 1 E-mail regarding prior.n. <o:p></o:p></p><p class=MsoNormal>My question is: <o:p></o:p></p><p class=MsoNormal>Is there a way to find the optimal value for prior.n – and how is this evaluated? I’m thinking of subtracting the raw variance from the calculated tagwise variance, and then look at the absolute SUM (the sum of error). Is this a good way to go?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Regarding the d$tagwise.dispersion (here d is a DGEList after estimateTagwiseDisp). I believe the object is a vector, but there are no row names. My question is now if the order of d$tagwise.dispersion is the same as rownames(d$counts)?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Session info:<o:p></o:p></p><p class=MsoNormal>R version 2.13.0 (2011-04-13)<o:p></o:p></p><p class=MsoNormal>Platform: x86_64-pc-mingw32/x64 (64-bit)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>other attached packages:<o:p></o:p></p><p class=MsoNormal>[1] edgeR_2.2.5<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Kind regards <o:p></o:p></p><p class=MsoNormal>Mads Sønderkær<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><b><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'><img width=190 height=36 id="Billede_x0020_1" src="cid:image001.jpg@01CC1EA5.94AFAD40" alt="Description: Description: http://aaudesign.aau.dk/GetAsset.action?contentId=4159292&assetId=4165759"><u><o:p></o:p></u></span></b></p><p class=MsoNormal><b><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Mads Sønderkær <o:p></o:p></span></b></p><p class=MsoNormal><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>PhD Student<br>Mobile: +45 3053 2492<o:p></o:p></span></p><p class=MsoNormal><b><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Aalborg University<o:p></o:p></span></b></p><p class=MsoNormal><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Department of Biotechnology, Chemistry and Environmental Engineering <o:p></o:p></span></p><p class=MsoNormal><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Sohngaardsholmsvej 49<o:p></o:p></span></p><p class=MsoNormal><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Room 17<o:p></o:p></span></p><p class=MsoNormal><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>9000 Aalborg<o:p></o:p></span></p><p class=MsoNormal><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Denmark<o:p></o:p></span></p><p class=MsoNormal><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'>Phone: +45 9940 8461<o:p></o:p></span></p><p class=MsoNormal><span lang=DA><a href="http://www.bio.aau.dk/"><span style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:blue'>www.bio.aau.dk</span></a></span><span lang=DA style='font-size:7.5pt;font-family:"Verdana","sans-serif";color:#1F497D'> <o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>