[R] Post Hoc tests for ANOVA

Richard M. Heiberger rmh at temple.edu
Fri Oct 19 17:23:25 CEST 2012

Please look at the ?mmc example for two-way ANOVA in library(HH).

If you don't already have HH you can get it with

mmc uses the glht function in the multcomp package for its calculations
and then draws the MMC graph.


On 10/19/12, Amartya <amartya916 at gmail.com> wrote:
> Hi,
> 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.
> Link-
> http://rtutorialseries.blogspot.com/2011/01/r-tutorial-series-two-way-anova-with.html
> b. Do TukeyHSD  on an aov model
> Link-
> http://www.r-bloggers.com/post-hoc-pairwise-comparisons-of-two-way-anova/
> 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
> Age).
> 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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