I've done a model design and I hope someone can help out with my understanding of it!
I have an experimental setup that looks something like this:
3 Time points (0hrs, 6hrs, 12hrs)
3 Different Conditions (Treatments A, B and C)
So that makes 9 different combinations of time points and treatments, each is in triplicate. There are therefore 27 Samples.
My design formula is : ~ Treatment + TimePoint + Treatment:TimePoint
My current understanding is this will give me small pValues of Treatment-specific effects over time?
I wanted to further refine this and look at a specific treatment and how it differs between two time points. So I used the following line:
foo <- list(c(“TreatmentA.TimePoint12hrs"), c(“TreatmentA.TimePoint0hrs"))
resMFType <- results(dds, contrast=foo)
Is this correct?