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  • chariko
    Member
    • Jun 2010
    • 56

    Strange results Deseq2 no adjusted p values or even p values

    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
    Senior Member
    • Aug 2009
    • 245

    #2
    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
    Michael Black, Ph.D.
    ScitoVation LLC. RTP, N.C.

    Comment

    • chariko
      Member
      • Jun 2010
      • 56

      #3
      Thanks a lot for your answer, mbblack. You are right, that was my case.

      Comment

      • Michael Love
        Senior Member
        • Jul 2013
        • 333

        #4
        hi, you can also check the FAQ of the DESeq2 vignette:

        vignette("DESeq2")

        Comment

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