Shan Gao you have sent me your file "expression-qwei.txt". The code that you posted in your initial mail could not possibly have worked with it, since it contains 3 columns, while your 'conditions' vector only has length 2. I have run the below script (which approximates as much as I could tell what you claimed you did) without problem. Its output is also posted below, as is the session info. I conclude that this was operator error, and there is no such bug in DESeq. I noted that your session info mentions a version of DESeq (1.6.1) that does not match your version of R (2.15.1). It seems that your R installation is messed up. Perhaps you can ask your system administrator to give you a correct installation of R and Bioconductor. Code: ----- library("DESeq") raw.data <- read.table("expression-qwei.txt", row.names=1) conditions = c("mutant","wild") counts = raw.data[, conditions] counts = counts[rowSums(counts) >= length(conditions)/2,] cds = newCountDataSet(counts, conditions) cds = estimateSizeFactors(cds) print(sizeFactors(cds)) cds = estimateDispersions(cds, method='blind') print(dispTable(cds)) cds = estimateDispersions(cds, method='blind', sharingMode='fit-only') print(dispTable(cds)) Output: ------- sessionInfo() mutant wild 1.075829 0.929516 mutant wild "blind" "blind" mutant wild "blind" "blind" > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin11.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq_1.8.3 locfit_1.5-8 Biobase_2.16.0 BiocGenerics_0.2.0 [5] fortunes_1.5-0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.1 DBI_0.2-5 IRanges_1.14.4 [4] RColorBrewer_1.0-5 RSQLite_0.11.1 XML_3.9-4 [7] annotate_1.34.1 genefilter_1.38.0 geneplotter_1.34.0 [10] grid_2.15.1 lattice_0.20-6 splines_2.15.1 [13] stats4_2.15.1 survival_2.36-14 xtable_1.7-0 On 7/29/12 7:30 PM, Wolfgang Huber wrote: > Dear Shan Gao > > thank you. I was not able to reproduce what you report, based on the > code below and a different data set. Can you please send us the data > file "expression-qwei.txt" (or any other data set that for you produces > this problem) together with the exact code that you ran (e.g. according > to the output of the R function 'history') ? > > Best wishes > Wolfgang > > > On 7/29/12 5:13 PM, wang peter wrote: >> 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 >> >> >> rm(list=ls()) >> library(DESeq) >> >> raw.data <- read.table("expression-qwei.txt",row.names=1) # >> counts <- raw.data[, 1:dim(raw.data)[2]]# >> conditions=c("mutant","wild") # >> counts <- counts[rowSums(counts) >= length(conditions)/2,]# >> cds <- newCountDataSet(counts, conditions)# >> >> #normalization >> cds <- estimateSizeFactors(cds) >> sizeFactors(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 >> LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 >> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 >> 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_1.6.1 locfit_1.5-8 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.32.3 AnnotationDbi_1.16.19 DBI_0.2-5 >> genefilter_1.36.0 geneplotter_1.32.1 grid_2.15.1 >> IRanges_1.12.6 >> [8] lattice_0.20-6 RColorBrewer_1.0-5 RSQLite_0.11.1 >> splines_2.15.1 survival_2.36-14 xtable_1.7-0 >>