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  • edgeR, "DGELIst" function, "group" parameter

    Hi,

    I am using edgeR for some RNASeq analysis. My question concerns the DGEList function and its "group" parameter. I realized that, whether doing group=mydesignfactor or group=rep(1,ncol(counts)), the cpm numbers that I get after
    counts.TMM <- calcNormFactors(counts.DGEList)
    cpm.TMM=cpm(counts.TMM, normalized.lib.sizes=TRUE)
    are strictly identical in either case. The only difference between both ways is that the counts.TMM$samples$group column duly reflects what I put in in "group".

    Is this normal? What is it that I am missing? Is the "group" nevertheless taken into account on the subsequent estimateGLMCommonDisp, estimateGLMTrendDisp, estimateGLMTagDisp, glmFit, glmLRT etc.?

    Thanks in advance for your help.

    Best,

    David Rengel

  • #2
    There's no reason that cpm should be dependent upon your experimental design (in fact, it shouldn't be). The various GLM function pay attention to the design, since that's where it's important.

    Comment


    • #3
      Hi dpryan,

      THanks for your reply. Yes, that is right. My only only doubt came from de fact that if normalized.lib.sizes=TRUE, then the cpm are calculated using the normalization factors, which I thought were somehow dependent on your experimental design, but it seems I was mistaken.

      David

      Comment


      • #4
        Correct, normalization factors are independent from experimental design.

        Comment


        • #5
          Thanks a lot!

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