I have 35 samples and 54374 genes such is the coding, do u think is it ok? #normalization dge <- calcNormFactors(dge) treatment=factor(c(rep('control',6),rep('treated',24),rep('control',5) )) time=factor(c('0h','0h','0h','24h','24h','24h','0h','0h','0h','6h','6h ','6h','6h','12h','12h','12h','12h','18h','18h','18h','18h', '24h','24h','24h','36h','36h','36h','48h','48h','48h','6h ','12h','18h','36h','48h')) design <- model.matrix(~treatment*time) dge <- estimateGLMCommonDisp(dge, design) dge <- estimateGLMTagwiseDisp(dge, design) Warning message: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max iterations exceeded > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.4.6 limma_3.10.3 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

It would appear that one gene out of 54374 has received a dispersion estimate that has not fully converged. That is very unlikely to affect your overall results. In the devel version of edgeR, to become the release version in October, this warning will no longer occur, because we now compute the maximum of the spline interpolant exactly. Best wishes Gordon > Date: Sun, 29 Jul 2012 11:13:06 -0400 > From: wang peter <wng.peter at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] a warining from edgeR > > I have 35 samples and 54374 genes > > such is the coding, do u think is it ok? > > > > #normalization > dge <- calcNormFactors(dge) > > treatment=factor(c(rep('control',6),rep('treated',24),rep('control', 5))) > time=factor(c('0h','0h','0h','24h','24h','24h','0h','0h','0h','6h',' 6h','6h','6h','12h','12h','12h','12h','18h','18h','18h','18h', > '24h','24h','24h','36h','36h','36h','48h','48h','48h','6 h','12h','18h','36h','48h')) > design <- model.matrix(~treatment*time) > > dge <- estimateGLMCommonDisp(dge, design) > dge <- estimateGLMTagwiseDisp(dge, design) > > > > Warning message: > In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : > max iterations exceeded > > > > > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_2.4.6 limma_3.10.3 > > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}