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 |