i have two sample, one is wild, the other is mutant i met a very wired problem when i set parameter sharingMode = "fit-only", such coding cannot work but if i set sharingMode=default, it can work and then i updated the packages, the problem still exists. rm(list=ls()) library(DESeq) raw.data <- read.table("expression-qwei.txt",row.names=1) counts <- raw.data[, 2:dim(raw.data)[2]] length<-raw.data[, 1] conditions=c("mutant","wild") counts <- counts[rowSums(counts) >= length(conditions)/2,] cds <- newCountDataSet(counts, conditions) lib_size <- read.table("lib_size_qwei.txt"); lib_size <- unlist(lib_size) cds <- estimateSizeFactors(cds) cds <- estimateDispersions(cds, method = "blind"?sharingMode="fit- only") > dispTable(cds) [1] NA NA cds <- estimateDispersions(cds, method = "blind") > dispTable(cds) mutant wild "blind" "blind" > 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] DESeq_1.8.3 BiocInstaller_1.4.7 locfit_1.5-8 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] annotate_1.34.1 AnnotationDbi_1.18.1 DBI_0.2-5 genefilter_1.38.0 geneplotter_1.34.0 [6] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 RColorBrewer_1.0-5 RSQLite_0.11.1 [11] splines_2.15.1 stats4_2.15.1 survival_2.36-14 tools_2.15.1 XML_3.9-4.1 [16] xtable_1.7-0 -- 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