hi Abhishek,

check out the ?results man page:

"By default, independent filtering is performed to select a set of genes
which will result in the most genes with adjusted p-values less than a
threshold, alpha. The adjusted p-values for the genes which do not pass the
filter threshold are set to NA."

also section 1.4.2 in the vignette:

"The results for particular genes can be set to NA, for either one of the
following reasons: ..."

hope this helps,

Mike



On Wed, Nov 20, 2013 at 9:16 PM, Abhishek Pratap <apratap@sagebase.org>wrote:

> Hi Michael and Simon
>
> I am starting to use DESeq2 on a 60 sample count data and seeing it report
> NA p-values for multiple genes. Not sure if this is due to cooks distance
> or some other thing. I did see the seqanswer thread to turn off cooks
> distance but dint work for me in DESeq2
>
>
> Copying just one example.. unfortunately the formatting will be messed up.
> Let me know if there is a good place to copy it for easier reading.
>
> Thanks!
> -Abhi
>
>     baseMean log2FoldChange     lfcSE      stat       pvalue       padj
>   SYMBOL
> 16012 58 5.556873e+01      1.4310814 0.2586475  5.532941           NA
>   NA
>
>
> mcols(diff_exp_result)[16012,]
>
> DataFrame with 1 row and 23 columns
>    baseMean   baseVar   allZero dispGeneEst dispGeneEstConv   dispFit
> dispersion  dispIter  dispConv dispOutlier   dispMAP Intercept
>   <numeric> <numeric> <logical>   <numeric>       <logical> <numeric>
>  <numeric> <numeric> <logical>   <logical> <numeric> <numeric>
> 1  1.437498  3.786966     FALSE    1.302189            TRUE  1.987536
> 1.404384         8      TRUE       FALSE  1.404384 0.2919642
>   condition_high_vs_low SE_Intercept SE_condition_high_vs_low
> WaldStatistic_Intercept WaldStatistic_condition_high_vs_low
>               <numeric>    <numeric>                <numeric>
> <numeric>                           <numeric>
> 1             0.3913094    0.3133799                0.2582543
> 0.9316622                             1.51521
>   WaldPvalue_Intercept WaldPvalue_condition_high_vs_low  betaConv  betaIter
>  deviance  maxCooks
>              <numeric>                        <numeric> <logical> <numeric>
> <numeric> <numeric>
> 1            0.3515111                        0.1297193      TRUE         6
>  184.0293 0.5676499
>
>
>
>
>
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] synapseClient_0.32-1                     getopt_1.20.0
>            TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
>  [4] GenomicFeatures_1.14.0                   GGally_0.4.4
>             pheatmap_0.7.7
>  [7] gplots_2.12.1                            RColorBrewer_1.0-5
>             Rsamtools_1.14.1
> [10] Biostrings_2.30.1                        gdata_2.13.2
>             reshape_0.8.4
> [13] plyr_1.8                                 ggplot2_0.9.3.1
>            DESeq2_1.2.5
> [16] RcppArmadillo_0.3.920.1                  Rcpp_0.10.6
>            GenomicRanges_1.14.3
> [19] XVector_0.2.0                            IRanges_1.20.5
>             org.Hs.eg.db_2.10.1
> [22] RSQLite_0.11.4                           DBI_0.2-7
>            AnnotationDbi_1.24.0
> [25] Biobase_2.22.0                           BiocGenerics_0.8.0
>             BiocInstaller_1.12.0
>
>         [[alternative HTML version deleted]]
>
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