I have a Group (A, B unequal sample size) x Condition1 (C, D) x Condition2 (E, F) design in which Group is a between subject factor and Conditions 1 and 2 are within subject factors.
I have run the group analysis using GroupAna and have noticed that when I look at a within subject contrast Group A, Condition1: C > D the regions that show up are different than if I run 3dANOVA3 within Group A and look at the Condition1 C>D.
I assume this difference is due to differences in df when running the between group vs. within group analysis. Is this correct?
Which way is the more appropriate way to describe the within group differences?