Suppose that I've a data with a total of 30,000 observations. Each observation has a total of 6 values, 3 per condition. I'm interested in, let's say, testing if the means of these two conditions for each of these observations are different or not. For this, we typically apply a statistical test of choice to each of these 30K observations. In order to control the false positive rate due to multiple testing, we'd control for FDR at say 5% using BH method.
Example of an observation would be:
# dummy data Condition 1: 40, 55, 48 Condition 2: 129, 77, 181
Also, let's assume I obtained a total of 1000 "significant" results. If I filter the data somehow, say, remove all those observations where the maximum value across all 6 values is < 5 and end up with a filtered set of 20K observations, then I find that the number of significant results is a bit higher, say 1250. If I continue this approach of filtering data with higher and higher thresholds (< 10, < 20 ... preferably using quantile = 0.1, 0.2, 0.3 etc..), I find that the number of significant results at 5% FDR keeps increasing up to a certain point and with too stringent filtering starts to reduce again.
It's fairly obvious that in controlling the FP in a multiple testing setup one compromises for the statistical power. My question is, are there methods that could somehow compute a filtering criteria which maximises the power (to detect after FDR correction)? If not, is it statistically sound approach to try and filter data with more than 1 value and decide on the one that maximises significance?