title: Post Hoc tests for ANOVA
body: <p>I was trying to figure out how to do  post-hoc tests for Two Way ANOVAs and found the following 2 approaches:</p>
  
  <ol>
  <li>Do pairwise t-tests (bonferroni corrected) if one finds significance with the ANOVA.
  Link- <a href="http://rtutorialseries.blogspot.com/2011/01/r-tutorial-series-two-way-anova-with.html" rel="nofollow">http://rtutorialseries.blogspot.com/2011/01/r-tutorial-series-two-way-anova-with.html</a></li>
  <li>Do TukeyHSD  on an aov model
  Link- <a href="http://www.r-bloggers.com/post-hoc-pairwise-comparisons-of-two-way-anova/" rel="nofollow">http://www.r-bloggers.com/post-hoc-pairwise-comparisons-of-two-way-anova/</a></li>
  </ol>
  
  <p>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).</p>
  
  <p>I have a few questions:</p>
  
  <ol>
  <li>Is the first method completely incorrect as hinted in the second link?</li>
  <li>What is the right way to do Bonferroni corrected post hoc tests for Two Way ANOVA in R?</li>
  <li>Does anyone know how post hoc tests for SPSS work in the case of Two Way ANOVAs (Univariate analysis)? Especially for Bonferroni corrected tests.</li>
  </ol>
  
  <p>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. </p>