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  • Simple effects in DESeq2

    Hello, this is probably a very simple point, but I want to make sure I understand this. In the DESeq2 ?results document it lists the following example (and comment):

    ## Example 2: two conditions, two genotypes, with an interaction term

    dds <- makeExampleDESeqDataSet(n=100,m=12)
    dds$genotype <- factor(rep(rep(c("I","II"),each=3),2))
    design(dds) <- ~ genotype + condition + genotype:condition
    dds <- DESeq(dds)
    resultsNames(dds)

    # Note: design with interactions terms by default have betaPrior=FALSE

    # the condition effect for genotype I (the main effect)
    results(dds, contrast=c("condition","B","A"))


    QUESTION:
    1. shouldn't what is called "the condition effect for genotype I (the main effect)" be called the simple effect for condition on genotype I?? The term "main effect" I am not sure is appropriate here as we are not averaging over all genotypes.
    2. If (1) is correct, how would one specify on DESeq2 a real main effect of B vs A averaged over all genotypes?

    Thank you,
    Ramiro
    Last edited by ramiro2k; 05-16-2017, 08:42 AM.

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