Re: [R] ok to use glht() when interaction is NOT significant?

From: Bert Gunter <>
Date: Mon, 07 Mar 2011 21:20:11 -0800

Inline below

On Mon, Mar 7, 2011 at 8:08 PM, array chip <> wrote:
> Hi, let's say I have a simple ANOVA model with 2 factors A (level A1 and A2) and
> B (level B1 and B2) and their interaction:
> aov(y~A*B, data=dat)
> It turns out that the interaction term is not significant (e.g. P value = 0.2),
> but if I used glht() to compare A1 vs. A2 within each level of B, I found that
> the comparison is not significant when B=B1, but is very significant (P<0.01)
> when B=B2.
> My question is whether it's legal to do this post-hoc comparison when the
> interaction is NOT significant? Can I still make the claim that there is a
> significant difference between A1 and A2 when B=B2?

(I am serious here). Don't know what "legal" means. Why do you want to make the claim? When does it **ever** mean anything scientifically meaningful to make it? What is the **scientific** question of interest? Are the data unbalanced? Have you plotted the data to tell you what's going on?

Warning: I come from the school (maybe I'm the only student...) that believes all such formal post hoc comparisons are pointless, silly, wastes of effort. Note the word: "formal" -- that is pretending the P values mean anything, For exploratory purposes, which can certainly include producing P values as well as graphs, such post hoc comparisons might lead to great science. It's the "formal" part that I reject and that you seem to be hung up on.

Note also: If you're a Bayesian and can put priors on everything, you can spit out posteriors and Bayes factors to your heart's content. Really! -- no need to sweat multiplicity even. Of course, I speak here only as an observer, having never actually inhaled myself.*


*Apologies to all non-US and younger readers. This is a smart-aleck reference to an infamous dumb remark from a recent famous, smart former U.S. president. Google "never inhaled" for details.

> Thanks
> John
>        [[alternative HTML version deleted]]
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Bert Gunter
Genentech Nonclinical Biostatistics

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Received on Tue 08 Mar 2011 - 05:27:17 GMT

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