Question: DESeq2 returning NA pvalue when counts are not zero
5.6 years ago by
Guest User • 12k
Guest User • 12k 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:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  DESeq2_1.0.19 RcppArmadillo_0.3.910.0 Rcpp_0.10.4  lattice_0.20-23 Biobase_2.20.1 GenomicRanges_1.12.5  IRanges_1.18.3 BiocGenerics_0.6.0 loaded via a namespace (and not attached):  annotate_1.38.0 AnnotationDbi_1.22.6 DBI_0.2-7 genefilter_1.42.0  grid_3.0.1 locfit_1.5-9.1 RColorBrewer_1.0-5 RSQLite_0.11.4  splines_3.0.1 stats4_3.0.1 survival_2.37-4 XML_3.98-1.1  xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
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