HELLO all: hope some one can help me on such error. > d <- DGEList(counts = d, lib.size = lib_size) > #normalization > dge <- calcNormFactors(d) > rm(d) > > fac=factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0h ','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h','t 18h','t18h', + 't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48h' ,'t48h','c6h','c12h','c18h','c36h','c48h')) > design = model.matrix(~fac) > colnames(design) <- levels(fac) > dge <- estimateGLMCommonDisp(dge, design)#??tag wise????????common?? > dge <- estimateGLMTagwiseDisp(dge, design) > glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion)#??????tag wise?? > t0_c0 = makeContrasts("t0h-c0h",levels=design) > lrt.dge <- glmLRT(dge, glmfit.dge, contrast = t0_c0) > result <- topTags(lrt.dge, n=dim(dge)[1], adjust.method="BH", sort.by="p.value") Error in abs(object$table$logFC) : Non-numeric argument to mathematical function 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_2.6.10 limma_3.12.1 -- 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

On 08/26/2012 12:52 PM, wang peter wrote: >> d <- DGEList(counts = d, lib.size = lib_size) >> >#normalization >> >dge <- calcNormFactors(d) >> >rm(d) >> > >> >fac=factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t 0h','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h', 't18h','t18h', > + 't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48 h','t48h','c6h','c12h','c18h','c36h','c48h')) >> >design = model.matrix(~fac) >> >colnames(design) <- levels(fac) >> >dge <- estimateGLMCommonDisp(dge, design)#??tag wise????????common?? >> >dge <- estimateGLMTagwiseDisp(dge, design) >> >glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion)#??????tag wise?? >> >t0_c0 = makeContrasts("t0h-c0h",levels=design) >> >lrt.dge <- glmLRT(dge, glmfit.dge, contrast = t0_c0) provide the _vector_ rather than matrix to contrast lrt.dge <- glmLRT(dge, glmfit.dge, contrast = t0_c0[,1]) (this is a subtle issue in glmLRT, where with contrast as a matrix argument, in tab <- data.frame(logFC = logFC, logCPM = (glmfit$abundance + log(1e+06))/log(2), LR = LR, PValue = LRT.pvalue, row.names = rn) logFC is also a matrix and 'tab' has first column named after the matrix column, rather than 'logFC'). Martin >> >result <- topTags(lrt.dge, n=dim(dge)[1], adjust.method="BH", sort.by="p.value") -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793