I refer to section 3.3.2 on nested interaction formulas in the edgeR user guide.
I wonder if the coefficient TreatDrug.Time.1h provides the logFC and associated FDR corresponding to (drug.1h-drug.0h)-(placebo.1h-placebo.0h). Is this interpretation correct?
Does it make sense to use nested interaction formulas when I have only one replicate for each level of Time and Treatment. In your example placebo.0h has two samples.
My study has one sample for each combination of the levels of two factors.Applying nested interaction formulas, all genes reported FDR = 1. I wonder if this result is due to the absence of replicates.
Might you suggest, alternatively, other ways where I can test the influence of multiple factors in differential expression results in presence of just one replicate for each combination of their levels?