Hi, I ran the pasilla dataset as outlined in the DESeq2 manual. For genes with zero counts, statistical testing is not performed and p values are NA. However, I noticed there are a number of genes for which their normalized counts are non-zero, but p values are still NA (refer to example below)? May I know why is this the case? > normalizedCounts <- t( t(counts(dds)) / sizeFactors(dds) ) > normalizedCounts["FBgn0000258", ] treated1fb treated2fb treated3fb untreated1fb untreated2fb untreated3fb untreated4fb 922.8067 452.6028 361.6749 738.0980 675.2863 391.9771 392.9846 > res["FBgn0000258", ] baseMean log2FoldChange lfcSE pvalue padj <numeric> <numeric> <numeric> <numeric> <numeric> FBgn0000258 562.2043 0.06053945 0.271575 NA NA Thank you very much! -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.0.19 RcppArmadillo_0.3.910.0 Rcpp_0.10.4 [4] lattice_0.20-23 Biobase_2.20.1 GenomicRanges_1.12.5 [7] IRanges_1.18.3 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.6 DBI_0.2-7 genefilter_1.42.0 [5] grid_3.0.1 locfit_1.5-9.1 RColorBrewer_1.0-5 RSQLite_0.11.4 [9] splines_3.0.1 stats4_3.0.1 survival_2.37-4 XML_3.98-1.1 [13] xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.

hi, This is discussed in Section F: Count outlier detection, of the vignette for version 1.0.z of DESeq2. You can turn this behavior off by setting cooksCutoff to FALSE for the function nbinomWaldTest (which can be run immediately after DESeq(), or after estimateSizeFactors and estimateDispersions). The documentation and control of this is better organized in the upcoming version 1.2.0, where the cooksCutoff argument moved to the results() function. best, Mike On Wed, Sep 25, 2013 at 5:26 AM, Ying Ying Sung [guest] < guest@bioconductor.org> wrote: > > Hi, > > I ran the pasilla dataset as outlined in the DESeq2 manual. For genes with > zero counts, statistical testing is not performed and p values are NA. > However, I noticed there are a number of genes for which their normalized > counts are non-zero, but p values are still NA (refer to example below)? > May I know why is this the case? > > > normalizedCounts <- t( t(counts(dds)) / sizeFactors(dds) ) > > normalizedCounts["FBgn0000258", ] > > treated1fb treated2fb treated3fb untreated1fb untreated2fb > untreated3fb untreated4fb > 922.8067 452.6028 361.6749 738.0980 675.2863 > 391.9771 392.9846 > > > res["FBgn0000258", ] > > baseMean log2FoldChange lfcSE pvalue padj > <numeric> <numeric> <numeric> <numeric> <numeric> > FBgn0000258 562.2043 0.06053945 0.271575 NA NA > > Thank you very much! > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] DESeq2_1.0.19 RcppArmadillo_0.3.910.0 Rcpp_0.10.4 > [4] lattice_0.20-23 Biobase_2.20.1 GenomicRanges_1.12.5 > [7] IRanges_1.18.3 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationDbi_1.22.6 DBI_0.2-7 > genefilter_1.42.0 > [5] grid_3.0.1 locfit_1.5-9.1 RColorBrewer_1.0-5 > RSQLite_0.11.4 > [9] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > XML_3.98-1.1 > [13] xtable_1.7-1 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]