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Table 4 Results of the simulation study: Differences between the p-values of the original two-part test and the two-part permutation test for data sets with small p-values (i.e. p-value of the original test ≤ 0.1), a positive difference means that the two-part permutation test has a smaller p-value than the original test; p1 and p2 are the probabilities for zero values and the positive values in group 1 are shifted by μ; 5,000 data sets with n1 = n2 = 10 were generated for each configuration

From: Two-part permutation tests for DNA methylation and microarray data

Configuration Number of data sets Mean difference (± SD) Median difference Quartiles of the difference
p1 = p2 = 0, μ = 2.5 4538 0.0118 (± 0.0145) 0.0057 0.0013, 0.0161
p1 = p2 = 0.3, μ = 2.5 4038 0.0008 (± 0.0069) 0.0020 0.0008, 0.0033
p1 = 0.4, p2 = 0.2, μ = 2.5 4346 0.0010 (± 0.0059) 0.0019 0.0008, 0.0033
p1 = 0.2, p2 = 0.4, μ = 2.5 4270 0.0011 (± 0.0056) 0.0018 0.0006, 0.0030
p1 = 0, p2 = 0.3, μ = 2.5 4883 0.0039 (± 0.0055) 0.0020 0.0005, 0.0051
p1 = 0.3, p2 = 0, μ = 2.5 4893 0.0040 (± 0.0053) 0.0022 0.0007, 0.0049
p1 = 0, p2 = 0.4, μ = 0 3427 -0.0033 (± 0.0119) 0.0006 -0.0092, 0.0029
cutoff value = 0.5, μ = 2.5 4621 0.0059 (± 0.0081) 0.0034 0.0009, 0.0072
cutoff value = 1, μ = 2.5 4860 0.0017 (± 0.0052) 0.0013 0.0003, 0.0032