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  • DESeq: condition A vs condition B

    How does DESeq which columns to assign to condition A and which to assign to column B? I previously ran an analysis in which column A corresponded to samples from males and column b corresponded to samples from females. This time around, it just so happens that column A corresponds to females and B to males. This is problematical for comparing datasets (for fold-change comparisons) so I tried to force DESeq to assign A to females using the following command:

    res = nbinomTest( cds, "male", "female" )

    but this did not have the intended effect (i.e. there was no change) - "A" is still females. Is there any way to specify how the program defines the conditions, aside from re-ordering the columns in the input table?

  • #2
    1.3.6 Note on factor levels
    By default, R will choose a reference level for factors based on alphabetical order. Then, if you never tell the
    DESeq2 functions which level you want to compare against (e.g. which level represents the control group),
    the comparisons will be based on the alphabetical order of the levels. There are two solutions: you can either
    explicitly tell results which comparison to make using the contrast argument (this will be shown later), or
    you can explicitly set the factors levels. Setting the factor levels can be done in two ways, either using factor:

    dds$condition <- factor(dds$condition, levels=c("untreated","treated"))

    ...or using relevel, just specifying the reference level:

    dds$condition <- relevel(dds$condition, ref="untreated")

    DESeq2 manual

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