[R] Post Hoc tests for ANOVA

Amartya amartya916 at gmail.com
Fri Oct 19 09:25:22 CEST 2012


I was trying to figure out how to do  post-hoc tests for Two Way ANOVAs and
found the following 2 approaches:

a. Do pairwise t-tests (bonferroni corrected) if one finds significance with
the ANOVA.

b. Do TukeyHSD  on an aov model 

Running the data set given in the first example in SPSS gives significant
pairwise difference for Treatment and Age (Treatmen and Age were the
independent variables) , while using the directions given in the first link
didn't give me significant pairwise different for Treatment (only gave for

I have a few questions:

a. Is the first method completely incorrect as hinted in the second link? 
b. What is the right way to do Bonferroni corrected post hoc tests for Two
Way ANOVA in R? 
c. Does anyone know how post hoc tests for SPSS work in the case of Two Way
ANOVAs (Univariate analysis)? Especially for Bonferroni corrected tests.

I am new to R, so please let me know if I made a mistake in framing the
question; I will try to elucidate as much as I personally can. Thanks for
your help.

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