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Table 1 p-values of the original two-part test and the two-part permutation test for seven regions in lung cancer cell lines; DNA methylation data from Siegmund et al. [4]

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

Region Original two-part test Two-part permutation test1
CALCA p = 0.0005 p = 0.0004
PTGS2 p = 0.0002 p = 0.0001
MTHFR p = 0.0007 p = 0.0002
MGMT-M1 p = 0.0860 p = 0.0857
APC p = 0.1684 p = 0.1712
MYOD1 p = 0.0132 p = 0.0111
ESR1 p = 0.0040 p = 0.0030
  1. 1performed based on simple random samples of 20,000 permutations (when using 20,000 permutations a 95%-confidence interval for the p-value is the observed p-value ± 0.007 when p = 0.5, or ± 0.003 when p = 0.05).