I have seen comments here stating you can use a two-way ANOVA to get the deltadeltaCts. Let's say your setup does not necessitate a two-way ANOVA but simply a one-way ANOVA - won't this test give me deltadeltaCt values and CIs as well?
Yes, that's correct.
Actually, "ANOVA" is not the right term here. What you mean are "linear models", and the ANOVA is based on such linear models. An analogy: if the linear models is a car, then the ANOVA is a crash test; the ANOVA will only tell you if the car will break under certain conditions, but the real thing that takes you over the road is the car.
The coefficients in a one-factorial model (using dCt as response) are ddCt values.
Note that the coefficient for the interaction of two factors is a dddCt value (the difference between ddCt values).
Final note: If you calculate dCt as Ct[ref] - Ct[goi], positive ddCt values will indicate induction, negative ddCt values will indicate repression.
Thank you Jochen, I was hoping to get a response from you specifically, cheers.
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