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I have a regression model with two significant main effects and a significant interaction. I'd like to calculate an effect size for one of the main effects.

I'm using the package compute.es in R. I'm not sure whether I should use the empirical means and standard deviations or the t-value from the regression model to calculate the effect size.

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You cannot do this. At least, not ONE effect size for all cases. That's what an interaction means.

That is, an interaction means that the effect of one IV is different at different levels of the other variable.

So, you could calculate the effect of one variable at any particular level of the other.

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