[R] quick ANOVA question

S Ellison S.Ellison at LGCGroup.com
Tue Nov 29 17:13:53 CET 2011

> -----Original Message-----
> What I like to know is if I apply an ANOVA to this data and 
> choose the control group as the reference group (using the 
> relevel function) what groups exactly are compared? Are only 
> all treated groups 1, 2, 3 tested against the control group 
> or are all possible combinations tested?

ANOVA doesn't compare one level against another; it compares all levels against none. *

lm() coefficients and associated p-values can be used to compare treatments to the 'control' if you use treatment contrasts with 'control' as the first or 'base' level and there are no other effects in the model. 

But see fortune(242). It may not apply to you, but it always applies to me at least to the extent that I am never quite sure that it doesn't.

S Ellison

*Ish. A more accurate description might be that anova in R compares a model with two or more levels specified for a factor to a model with no levels specified other than the default intercept. But that doesn't have as nice a ring to it, does it?
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