[BioC] DESeq analysis

[narges [guest]]

Hi all

I am doing some RNA seq analysis with DESeq. I have applied the nbinomTest to my dataset which I know have many differentially expressed genes but the first problem is that the result values for "padj"column is almost NA and sometimes 1. and when I want to have a splice from my fata frame the result is not meaningful for me.

 -- output of sessionInfo(): 

res <- nbinomTest(cds, "Male", "Female")

> head(res)
               id   baseMean baseMeanA  baseMeanB foldChange log2FoldChange
1 ENSG00000000003  0.1130534  0.000000  0.2261067        Inf            Inf
2 ENSG00000000005  0.0000000  0.000000  0.0000000        NaN            NaN
3 ENSG00000000419 14.3767155 17.162610 11.5908205  0.6753530     -0.5662863
4 ENSG00000000457 17.0174761 15.342800 18.6921526  1.2183013      0.2848710
5 ENSG00000000460  3.9414822  2.855099  5.0278659  1.7610131      0.8164056
6 ENSG00000000938 16.0894945 18.350117 13.8288718  0.7536122     -0.4081058
       pval padj
1 0.9959638    1
2        NA   NA
3 0.3208560    1
4 0.5942512    1
5 0.4840607    1
6 0.5409953    1


> res1 <- res[res$padj<0.1,]
> head(res1)
       id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
NA   <NA>       NA        NA        NA         NA             NA   NA   NA
NA.1 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.2 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.3 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.5 <NA>       NA        NA        NA         NA             NA   NA   NA

my first question is that why although I know there are some differentially expressed genes in the my data, all the padj values are NA or 1 and the second question is this "NA.1" , "NA.2", ..... which are emerged as the first column of object "res1"instead of name of genes 

Thank you so much 
Regards

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