Okay, I have a confession to make. I haven’t had time to write this section, but I think the method of planned comparisons is important enough to deserve a quick discussion. In our discussions of multiple comparisons, in the previous section and back in Chapter 14, I’ve been assuming that the tests you want to run are genuinely post hoc. For instance, in our drugs example above, maybe you thought that the drugs would all have different effects on mood (i.e., you hypothesised a main effect of drug), but you didn’t have any specific hypothesis about how they would be different, nor did you have any real idea about which pairwise comparisons would be worth looking at. If that is the case, then you really have to resort to something like Tukey’s HSD to do your pairwise comparisons.
The situation is rather different, however, if you genuinely did have real, specific hypotheses about which comparisons are of interest, and you never ever have any intention to look at any other comparisons besides the ones that you specified ahead of time. When this is true, and if you honestly and rigourously stick to your noble intentions to not run any other comparisons (even when the data look like they’re showing you deliciously significant effects for stuff you didn’t have a hypothesis test for), then it doesn’t really make a lot of sense to run something like Tukey’s HSD, because it makes corrections for a whole bunch of comparisons that you never cared about and never had any intention of looking at. Under those circumstances, you can safely run a (limited) number of hypothesis tests without making an adjustment for multiple testing. This situation is known as the method of planned comparisons, and it is sometimes used in clinical trials. In a later version of this book, I would like to talk a lot more about planned comparisons.