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I am in the process of testing my variances to see if I meet the assumptions of a two way ANOVA. While doing this, I was wondering exactly what I have to test.

For example, I used the Fligner Test to test the variances of the interaction: fligner.test(Pros_Width~interaction(Fouling,Sex),data=Pros_Fouling). Would I also need to test my independent variables by themselves such as :

fligner.test(Pros_Width~Sex)

fligner.test(Pros_Width~Fouling)

And if any of these 3 tests were significant, then I would not meet the assumptions of a two way ANOVA? Should I transform if not, or try to find a non-parametric version?

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