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Indeed, we can use a universal design, which is adapted to sensitivity analysis as well as optimization without any supplementary simulation.
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Supplementary simulations of the free-floating configuration were run to assess the effect of the discretization error (this error is controlled by the resolution of the computational mesh; the finer the mesh, the smaller the discretization error).
The effects are demonstrated empirically by an analysis of 7 of the largest microarray cancer outcome prediction datasets and supplementary simulations, and by contrasting them to prior analyses of the same data.
The full study benchmarking the performance of the model can be found in Supplementary Section 'Simulation study'.
The precision of the BBD approximation is discussed in supplementary material Simulation S1.
The resulting distribution reproduces the Poisson-binomial distribution nearly exactly and its P-values can be calculated with ease even for thousands of lists (see also supplementary material Simulation S1 for details on the precision of BBD).
Edge-swapping (1000 simulations, see above) was used to determine occurrence probabilities and gene co-occurrence was analyzed using module size 3 (co-occurrence of three genes), bi-binomial Z-score cutoff 6, bi-binomial P-value cutoff 1.0E-5, and support 5. Supplementary material Simulation S1 provides details on why module size 3 is chosen.
The performance of the algorithm has been studied extensively for artificial data (Supplementary Section 'Simulation study').
Supplementary text 1.1: Simulation methods.
Supplementary text 1.2: Simulation results.
Additional file 2: Supplementary figures for simulation study and for analysis of mice data.
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