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Table 3 Differences between the p-values of the original two-part test and the two-part permutation test for genes with at least one truncation and small p-values (i.e. the p-value of the original test must be as small as mentioned under condition), a positive difference means that the two-part permutation test has a smaller p-value than the original test; data from the microarray experiment of Tschentscher et al. [11]

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

Condition Number of remaining genes Mean difference (± SD) Median difference Quartiles of the difference
p ≤ 0.1 514 0.0065 (± 0.0126) 0.0047 0.0012, 0.0124
p ≤ 0.05 336 0.0057 (± 0.0064) 0.0040 0.0018, 0.0095
p ≤ 0.01 114 0.0025 (± 0.0018) 0.0019 0.0010, 0.0035
p ≤ 0.001 19 0.0006 (± 0.0003) 0.0006 0.0003, 0.0009