P.Mean: Can I please skip the Bonferroni adjustment? (created 2008-08-19).

I ran multiple correlation analysis for abundances, richness (species density), and diversity of different growth forms in four different landscapes in Colombian Amazonia. My questions is: Do I have to calculate a Bonferroni test to adjust for each probability?

I always get nervous about these questions where people seem to be wanting my permission to do something that they know is bad. Conducting multiple hypothesis tests without any adjustment to the alpha level is certainly considered bad by some. But you are actually off the hook, because there is no consensus in the research community about when to apply the Bonferroni correction. Certain disciplines use Bonferroni extensively and other use it rarely.

I suspect you don't want to use a Bonferroni adjustment because you lose some of your statistically significant results when this happens. So don't use it.

There are only two times when a Bonferroni adjustment is mandated. First, you must use a Bonferroni adjustment if you promised that you would in the original research protocol. Second, you must use the Bonferroni adjustment if someone in a position of authority over you demands it. This person could be your boss or someone who exercises control over whether you can publish your results (that is, a referee or a journal editor).

By the way, my opinion (don't use Bonferroni here) is not important, as I am not in a position of authority over you. When my grand plan to take over the world is realized, that will change, of course.

I would suggest that you re-run the analysis using a Bonferroni adjustment, but do not report it in your publication. Keep it available if a referee asks about this. In fact, it will impress the referee if you mention in your response that you had already run the analysis using Bonferroni. If the referee does not ask about Bonferroni, then all that you have lost is a little bit of time.

Of course, whether or not you use the Bonferroni adjustment, you should mention the large number of comparisons as a (minor) limitation in your discussion section.

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