[R] Post Hoc tests for ANOVA

rent0009 at umn.edu rent0009 at umn.edu
Fri Oct 19 17:30:47 CEST 2012

Amartya: This is probably more of a statistics question than an R question. 
I would go with the Tukey HSD, were I you as that is its intention.

Is there anyone in your organization (school, company, etc) that does 
statistical consulting? I have had wonderful experience working with the 
consulting clinic at the U of MN. If nothing else, buying a stats grad 
student some coffee might save you hours of headache in reading and 
searching message boards.


On Oct 19 2012, Amartya wrote:

>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 
>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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