Both the local FDR and the q-value are calculated for individual tests. The q-value should be preferred if all positive tests will be followed up with roughly equal priority, which may be the case for a moderately powered study in which true and false positives are not well separated. The local FDR is preferable if decisions to follow up positive tests are taken on a case by case basis, because it is a property of single tests rather than the whole set of positive tests. This applies if there are a few very strong associations, together with some moderate ones, or if additional sources of evidence, such as biological plausibility, are taken into account, together with the statistical association.
