Figure 6

Mean FDR curves for analyses of more complex experimental designs. Mean FDR curves, based on 100 simulations, comparing the performance of multiple methods in identifying more complex patterns of differential expression. The data are simulated from samples coming from three experimental conditions A, B and C, giving a total of five possible patterns of differential expression. We show here the false discovery rates for the identification of tuples where one experimental condition differs from the other two ({A₁, ..., A _n , B₁, ..., B _n } {C₁, ... C _n }) and for the identification of tuples where all three experimental conditions are different ({A₁, ..., A _n }{B₁, ... B _n }{C₁, ... C _n }). The data are simulated with varying number of libraries n in each experimental condition.