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  • edgeR: number of DGE genes and FDR??

    Hi all,

    In my concept, if the number obtained from "summary(de<-decideTestsDGE(df, adjust.method="BH", p.value=0.05))" is 7, then there should be 7 genes with FDR less than 0.05 in the list, right?
    When I tried to see DGE by edgeR, it present as following:

    > summary(de<-decideTestsDGE(df, adjust.method="BH", p.value=0.05))
    [,1]
    -1 2
    0 340
    1 5

    Here means that the number of differentially expressed gene is 7 (FDR<0.05), right?

    But when I wanted to see the top 20 genes, their FDR are all less than 0.05.

    > topTags(A_B,20)
    Comparison of groups: A-B
    logFC logCPM PValue FDR
    ATxxx 2.4277458852 11.707828 2.177741e-11 7.556760e-09
    ATxxx 2.1995419428 7.696531 4.090971e-06 7.097835e-04
    ATxxx 1.3143387328 12.547087 3.155543e-05 3.364114e-03
    ATxxx -1.4263203424 11.251632 3.877941e-05 3.364114e-03
    ATxxx 1.4985278106 11.174781 9.803395e-05 6.803556e-03
    BRODxx -3.0514440353 6.191085 1.635781e-04 9.460266e-03
    ATLANxx 0.8367554361 13.197904 4.059972e-04 2.012586e-02
    HELxx 1.5246704658 7.394363 2.432827e-03 1.055239e-01
    ATCxxx 0.8184084803 12.005165 3.088130e-03 1.190646e-01
    ATRxxx 2.3828224280 5.805848 3.581865e-03 1.242907e-01
    Sadxxx -1.4732584469 7.605255 5.243566e-03 1.605100e-01
    ATxxx -5.0018389997 4.633235 5.550776e-03 1.605100e-01
    .............................

    Did I misunderstand something?

  • #2
    You misunderstood scientific notation:

    1.055239e-01 = 0.1055239

    So there are 7 genes with FDR < 0.05 (fifth column).
    Last edited by bruce01; 03-12-2013, 08:21 AM.

    Comment


    • #3
      Originally posted by bruce01 View Post
      You misunderstood scientific notation:

      1.055239e-01 = 0.1055239

      So there are 7 genes with FDR < 0.05 (fifth column).
      Thanks for answering my stupid misunderstood!

      Comment


      • #4
        No problem, remember it like this:

        1.04e-01 means move the 1 one space back behind the decimal point = 0.104
        1.04e-02 means move the 1 two spaces =0.0104

        And so on. I still do that in my head every time I see sci. notation!

        Comment


        • #5
          Originally posted by bruce01 View Post
          No problem, remember it like this:

          1.04e-01 means move the 1 one space back behind the decimal point = 0.104
          1.04e-02 means move the 1 two spaces =0.0104

          And so on. I still do that in my head every time I see sci. notation!
          Thanks again!

          I had other 3 comparisons, but none of them list their FDR with sci. notation. Is that means they are too big and not necessary to use sci. notation, e.g. 0.000745?
          Last edited by SpreeFu; 03-12-2013, 08:58 AM.

          Comment

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