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  • Group sizes in RNA-seq DE

    Hi all,

    I would like to run an RNA differential expression analysis on two groups (two cancer subtypes) but my number of samples in the groups is not even close to equal.
    I have one group with about 120 samples and the other one has around 25 samples, is it O.K to run DEseq or EdgeR on such different size groups ? Would the possible bias be corrected somehow ? If not, What is the maximal group difference I can work with in DE?

    Thanks,

    Best,
    Moriah

  • #2
    any answer?

    Moriah,

    did you ever get an answer? I'm seeing that EdgeR actually generates errors and doesn't work for unequal samples. Is this a fundamental limitation?

    Will Nelson

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    • #3
      Having different group sizes in no problem, neither for DESeq nor for edgeR.

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