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.
>

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