Changes

*First look at the genotype:diet column. If this p-value is <0.05 then you have a significant interaction between genotype and diet. If this is the case move on to [[#No Main EffectInteraction]] to separate out your groups. If this value is >0.05 then there is no interaction, check if the p value for either of your groups is significant. If it is (and there is no interaction) then go ahead to [[#Main Efect]]. In the above example there is no interaction, but there are two main effects:

====No Main EffectInteraction====

TukeyHSTukeyHSD(wt.fit)</pre>This will tell you, separate from the interaction, whether each pairwise comparison is significant. You will have to repeat this by re-doing subset with each genotype and diet value as needed. Alternatively you can also account for the effect of one variable on the significance of the other. For example, if both diet and genotype interact, you may want to know what the effect of diet is, controlling for the effect of genotype. This is done like this:<pre>TukeyHSD(fit.aov, "diet") #This does pairwise comparisons of diet, while accounting for the effect of genotype