I am conducting a two-way ANOVA with 3 levels in factor A and 4 levels in factor B. In the case of significant interactions, which test I can use to answer the question of where are the significant differences?
PS: I know that I have to compare levels of each factor within each level of the other factor and vice versa.
The best approach is to use the lsmeans or emmeans function or option in the software you are using. This will allow you to compare e.m. means for the levels of the interaction (FactorA : FactorB), or to compare one factor within another (FactorA | FactorB). If you are using traditional OLS anova, and the design is completely balanced, the e.m. means will be the same as the arithmetic means. If not, e.m. means will take into account the other factors in the model.
I pretty much agree with the above suggestions. I will suggest a slightly different approach here. See the attachment for the details and location of the methods I prefer. Good luck to you, Best wishes David Booth
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