Inspired by, and related to, Meg’s recent poll on how you interpret interaction terms and main effects in ANOVA, I thought I’d ask my own ANOVA-related questions:
Part of the reason I’m asking these two questions is that different stats programs default to different calculation methods. Base R defaults to type I SS (though some packages have different defaults), while SAS defaults to type III. All of these methods give the same answer when the design is balanced (which is one good reason to balance your designs!), but they give different answers for unbalanced designs because they test different hypotheses. So really, what I’m asking is, exactly what hypotheses do you prefer to test when doing ANOVA with >1 factor?
I’m also curious whether people’s preferences match up with the defaults in their preferred stats packages. And if the match is because stats package defaults shape people’s preferences, rather than people’s preferences shaping their choice of stats package.