[BioC] DESeq2 returning NA pvalue when counts are not zero

[Ying Ying Sung [guest]]

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

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