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Old 05-16-2017, 07:34 AM   #1
ramiro2k
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Location: Vermont

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Default 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 at 08:42 AM.
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