Does anyone know how to calculate the eta squared value from a manova analysis in JMP? I know that the E and H matrices tab shows the sum of squares for each parameter, but which values do I use to calculate SStotal and SSeffect? In my model, I have 2 control variables (age and gender) and then a two way factorial. If only one of these variables (in addition to both control variables) is significant, and I have two dependent variables for the Manova, do I add all four SS values in the matrix for that particular independent variable to get the SSeffect?
Alternatively, is there a way to get effect sizes automatically generated in JMP with MANOVAs instead of trying to do it by hand?
Lastly, I have noticed that I get different p-values and SSs when running manovas in R vs JMP. Does anyone know why this is the case?
Any thoughts you have would be greatly appreciated!