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Table 2 Comparison of the relative sensitivity and specificity. Smoking-associated DMCs (sDMCs) were defined at FDR < 0.05 and FDR < 0.3 and for each of 5 methods in the 152 whole blood Illumina 450k samples from the MRC1946 birth cohort data

From: A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

nTP = 62, nTN = 89290 NoADJ EpiD (noDHS) EpiD CBS CP
FDR < 0.05      
 sDMCs 34 67 70 58 152
 | TP ∩ sDMC | 31 34 35 36 37
 Sensitivity 0.50 0.55 0.56 0.58 0.60
 FP = | TN ∩ sDMC | 0 3 3 0 11
 Specificity 1 0.999966 0.999966 1 0.999877
 Empirical FDR <0.03 0.045 0.043 <0.02 0.072
FDR < 0.3
 sDMCs 67 544 802 259 10457
 | TP ∩ sDMC | 40 50 52 44 54
 Sensitivity 0.64 0.81 0.84 0.71 0.87
 FP = | TN ∩ sDMC | 1 73 121 31 1735
 Specificity 0.99998 0.9992 0.998 0.9996 0.98
 Empirical FDR 0.01 0.13 0.15 0.12 0.17
  1. Methods are: NoADJ = no-adjustment, EpiD (noDHS) = adjustment with RPC using reference with no DHS info, EpiD = adjustment with RPC and a reference with DHS info, CBS = adjustment with CIBERSORT, CP = adjustment with constrained projection. Sensitivity was estimated as the fraction of the 62 gold-standard true positives (TP) found among the sDMCs. In the case of specificity, this was estimated as the fraction of true negatives (TN) among sDMCs measured relative to a gold-standard set of 89290 true negative (TN) CpGs