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Table 5 The performances of 6 joint tests based on HM27k data GSE37020 and GSE20080

From: Robust joint score tests in the application of DNA methylation data analysis

Test nSig nValidation nTV pTV(%) nFV pFV(%)
JointLRT 4556 2213 1705 77.0 508 23.0
KS 1288 60 47 78.3 13 21.7
AW 1850 262 220 84.0 42 16.0
iAW.Lev 2041 747 666 89.2 81 10.8
iAW.BF 1843 339 296 87.3 43 12.7
iAW.TM 1838 387 342 88.4 45 11.6
  1. nSig: the number of significant CpG sites detected in GSE37020 based on FDR adjusted p-value < 0.05;
  2. nValidation: the number of validated CpG sites in GSE20080 based on unadjusted p-value < 0.05;
  3. nTV: the number of truly validated CpG sites with the same difference directions in means and variances between the two groups;
  4. pTV: \(=\frac {nTV}{nValidation}\), the proportion of significant CpG sites detected in GSE37020 and truly validated in GSE20080;
  5. nFV: the number of falsely validated CpG sites in GSE20080 with inconsistent difference direction in means or variances between the two groups;
  6. pFV: \(=\frac {nFV}{nValidation}\), the proportion of significant CpG sites detected in GSE37020 but falsely validated in GSE20080