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  • EdgeR - default offset

    Greetings R aficionados!

    I was wondering whether anyone could tell me what the default offset is that is used in the glmFit function of EdgeR? Is it either the library size, or lib.size*norm.factor(from calcNormFactors)?

    Thanks for the help!

  • #2
    From the source code:

    Code:
    #       Check offset and lib.size
            if(is.null(offset)) {
                    if(is.null(lib.size)) lib.size <- colSums(y)
                    offset <- log(lib.size)
            }
    So, log(lib.size).

    Comment


    • #3
      If y is a matrix, then offset defaults to log(lib.size).

      If y is a DGEList, then offset defaults to y$offset if that is set, otherwise to log(lib.size*norm.factors). See getOffset.

      In other words, it defaults to whatever can be found in y.

      Comment


      • #4
        Thank you!

        Comment

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