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The p.adjust function in R can produce P value adjustments based on methods from Hochberg and Hommel, which are both more powerful than methods from Bonferroni and Holm. However, and as stated in the R documentation:

Hochberg's and Hommel's methods are valid when the hypothesis tests are independent or when they are non-negatively associated (Sarkar, 1998; Sarkar and Chang, 1997).

Can anyone explain what this means in a more accessible language?

Also, is there a way to empirically determine whether your hypothesis tests (data) meet this assumption?

kjetil b halvorsen
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Moose
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  • You might want to see my related question and whuber's answer at [Plain language meaning of "dependent" and "independent" tests in the multiple comparisons literature?](http://stats.stackexchange.com/questions/137337/plain-language-meaning-of-dependent-and-independent-tests-in-the-multiple-co) – Alexis Feb 27 '15 at 15:07

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