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Table 3 Time in seconds for p -value calculations for 6,303 gene sets in three genome-wide expression studies

From: Moment based gene set tests

Method Moran Zhang Scherzer
M=100 31.03 29.84 34.71
M=500 31.95 32.49 35.54
M=1,000,000 5010.17 4434.77 3933.15
Normal 29.74 27.00 34.66
Beta 30.79 31.88 37.89
M=30,000 9146.27 7217.59 11808.02
M=40,000 12256.54 9636.06 16545.60
M=50,000 16833.08 12564.06 21480.80
M=500,000 149588.37 129667.73 187067.91
χ 2 11020.62 10600.82 12677.15
  1. Linear statistic results with M = 100, M = 500, and M = 1,000,000 permutations, and the normal and beta approximations are in the top block. Timings for the quadratic statistic with M = 30,000, M = 40,000, M = 50,000, and M = 500,000 permutations, and the χ 2 approximation are presented in the bottom block.