FDR: Why 300 Tests Need BY

What does controlling the false discovery rate at q = 0.05 promise?

• Each admitted pair has at most a 5% chance of being false
• On average, no more than 5% of the admitted pairs are false
• At most 5% of all tested pairs are admitted

Gates 1 and 2 removed 24 of a fold's 300 candidate pairs. What is m for the FDR step?

• 300, the full universe of pairs
• 276, the number of pairs actually tested at Gate 3
• However many pairs passed a raw 5% test