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Table 3 CpG site-specific regression models before and after normalization step

From: Identifying and correcting epigenetics measurements for systematic sources of variation

Values Methods Significant sitesb CHARGEc Sensitivity 1-Specificity
β values Standard adjustmenta 444 357 (80%) 1.9×10−2 2.2×10−4
Residuals 427 365 (85%) 1.9×10− 2 1.5×10− 4
ComBat 600 411 (69%) 2.2×10− 2 4.7×10− 4
SVA 96 89 (92%) 0.5×10−2 0.2×10−4
M values Standard adjustmenta 322 274 (85%) 1.5×10−2 1.2×10−4
Residuals 332 299 (90%) 1.6×10−2 0.8×10−4
ComBat 387 335 (87%) 1.8×10−2 1.3×10−4
SVA 144 134 (93%) 0.7×10−2 0.2×10−4
  1. Models are adjusted for chip position, recruitment centre, the five percentages of leukocyte subtypes and age at recruitment, menopausal status and BC status
  2. aAlso adjusted for batch and sample position
  3. bNumber of significant sites for smoking status after p values FDR correction
  4. cNumber (and percentage) of significant sites identified by the CHARGE meta-analysis