title: R: Interpreting results from ANOVA and TukeyHSD analyses
body: <p>I have run an ANOVA and TukeyHSD over a dataframe containing anatomical regions in column 1 (region) and gene expression values in column 2 (S1). I normally would expect the p-value from the aov summary to be expressed as <strong>Pr(>F)</strong>, so I'm a little fuzzy on the results I've obtained. Also, can someone help me understand the Tukey multiple comparisons of means results? I'm not totally clear on what the <strong>diff</strong> and <strong>p adj</strong> results indicate. The results shown here are an abridged version of what I'm actually working with, FYI. </p>
  
  <pre><code>&gt; aov.result = aov(S1 ~ region, data=raw.data)
  &gt; summary(aov.result)
               Df  Sum Sq Mean Sq F value    Pr(&gt;F)    
  region       60  61.713 1.02856  5.9246 &lt; 2.2e-16 ***
  Residuals   655 113.712 0.17361                      
  ---
  Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
  &gt; TukeyHSD(aov.result)
  Tukey multiple comparisons of means
      95% family-wise confidence level
  
  Fit: aov(formula = S1 ~ region, data = raw.data)
  
  $region
                       diff           lwr          upr     p adj
  AB-AA        0.4118651583 -2.864195e-01  1.110149848 0.9847745
  AHA-AA      -0.0468785098 -7.608569e-01  0.667099930 1.0000000
  APir-AA      0.4419135565 -2.563711e-01  1.140198246 0.9502924
  B-AA         0.5379787168 -1.603060e-01  1.236263406 0.5846356
  </code></pre>