100 proteins changed 2-fold: impute sample minimum: mean false discovery proportion 2.5%, changed proteins found 44.9%, studies with any call 100.0%; impute down-shifted value: mean false discovery proportion 2.6%, changed proteins found 51.2%, studies with any call 100.0%; filter >= 3 valid per group, no imputation: mean false discovery proportion 3.2%, changed proteins found 63.2%, studies with any call 100.0%
No protein changed: impute sample minimum: mean false discovery proportion 9.6%, changed proteins found nan%, studies with any call 9.6%; impute down-shifted value: mean false discovery proportion 3.9%, changed proteins found nan%, studies with any call 3.9%; filter >= 3 valid per group, no imputation: mean false discovery proportion 1.6%, changed proteins found nan%, studies with any call 1.6%