If we had done a standard chip-wide association analysis on this data, none of the individual variants in this study would be significantly associated with AD after multiple comparisons corrections. In fact, the smallest Q-value would be 0.7 using the standard Benjamini-Hochberg procedure. However among our seven gene sets, four gene sets (norepinephrine, glutamate, GABA, and CRH) achieved a Q-value < 0.1.
