Strange results Deseq2 no adjusted p values or even p values

[chariko]

I analyzed a RNASeq experiment with EDGE-Pro and the statistical test was performed with Deseq2.
I obtained the following strange results for the statistical test for some genes (info regarding the number of counts for each sample is added):

-----; Fold Change; pvalue; padj; CONDITION_1; CONDITION_1; CONDITION_1; CONDITION_2; CONDITION_2; CONDITION_2
Gene1; -5.2; 0.003; NA; 0; 2; 0; 4; 5; 26
Gene2; -5.16; 0.004; NA; 2; 0; 0; 4; 4; 18
Gene3; -3.21; 0.019; NA; 5; 2; 2; 22; 3; 15
Gene4; -3.64; 0.024; NA; 1; 4; 1; 3; 5; 38
Gene5; -3.21; 0.031; NA; 8; 8; 5; 2; 2; 0
Gene6; 1.01; NA; NA; 786; 65; 42; 228; 119; 281
Gene7; -8.18; NA; NA; 5; 2; 4; 8; 6; 326
Gene8; -30.19; NA; NA; 16; 20; 0; 502; 415; 1192


My questions are:

1) Does anybody know why I do not obtain any padj value for any of the genes?
I wondered it was because for the presence of "0" but that does not match for all the cases (gene 3 and gene 4)

2) Why do I not obtain any p value for Gene 7 and 8? They have a high variability but in any case I supposse that would not affect the statistical test (at least the could have obtained a P=1)

Any clues would be appreciated,

[mbblack]

chariko - have a look through this thread as it should already give you the answer to your question - http://seqanswers.com/forums/showthread.php?t=45526

[chariko]

Thanks a lot for your answer, mbblack. You are right, that was my case.

[Michael Love]

hi, you can also check the FAQ of the DESeq2 vignette:

vignette("DESeq2")