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  • edgeR: very low p-value and very high variance within the group of replicates. What's

    I'm using `edgeR` in order to perform differential expression analysis from RNA-seq experiment.

    I have 6 samples of tumor cell, same tumor and same treatment: 3 patient with good prognosis and 3 patient with bad prognosis. I want to compare the gene expression among the two groups.

    I ran the `edgeR` pakage like follow:

    x <- read.delim("my_reads_count.txt", row.names="GENE")
    group <- factor(c(1,1,1,2,2,2))
    y <- DGEList(counts=x,group=group)
    y <- calcNormFactors(y)
    y <- estimateCommonDisp(y)
    y <- estimateTagwiseDisp(y)
    et <- exactTest(y)

    I obtained a very odd results: in some cases I had a very low *p*-value and FDR but looking at the raw data it is obvious that the difference between the two groups can't be significant.
    This is an example for `my_reads_count.txt`:

    GENE sample1_1 sample1_2 sample1_3 sample2_1 sample2_2 sample2_3
    ENSG00000198842 0 3 2 2 6666 3
    ENSG00000257017 3 3 25 2002 29080 4

    And for `my_edgeR_resulta.txt`:

    GENE logFC logCPM PValue FDR
    ENSG00000198842 9.863211e+00 5.4879462930 5.368843e-07 1.953612e-04
    ENSG00000257017 9.500927e+00 7.7139869397 8.072384e-10 7.171947e-07

    I would like that the variance within the group is considered. Does anyone may help me? Some suggestion?

  • #2
    The edgeR developers answered this question on the Bioconductor mailing list.

    Please don't ask the same question on multiple forums at the same time -- it forces us to either answer the same question twice or to leave a question looking as if it wasn't answered.

    Gordon

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