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I ran an Anova using the car package.

y~A*B+C

A has 2 factor levels, B has 3 factor levels, and C has 2 factor levels (data from two data sets was included in the analysis. C is Experiment 1/2)

I found that there is a significant effect of A and B but no significant interaction. I now wanted to do post hoc comparisons among the levels of factor B separately for each level of factor A, which is of interest to me. I did another Anova for each level of factor A (y~B+C) and now want to do a post hoc comparison to see differences among the 3 levels of factor B under each condition. However, there is clear heteroscedasticity in the residuals, which I corrected for using the white.adjust argument in the Anova. Is there a post hoc test that can be used for heteroscedastic data in e.g. the emmeans package?

Should I rather use weighted regression (e.g. gls) to resolve the heteroscedasticity issue and then do e.g. tukey adjusted comparisons?

Any advice is much appreciated!

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Yes. That is what you should do. emmeans() summarizes model results, so you need to hand it a model that you trust. See also the FAQ vignette in the emmeans package, which also discusses this matter.

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  • $\begingroup$ Many thanks for your fast reply. I assume you mean that I should rather go with weighted regression to fix the heteroscedasticity issue, as I cannot include a heteroscedasticity "correction" in the post hoc test, as I did for my Anova model. I will try a weighted gls model. Maybe that does the trick. I know that the games-howell post hoc test can be used for data that is heteroscedastic. Are there other post hoc tests? (more out of curiosity) $\endgroup$
    – Lizard2
    Dec 15, 2020 at 16:09

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