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Table 1 Values of weighted partial R2 (%) from PC-PR2 analysis indicating the proportion of variability of methylation levels, before and after normalization step, explained by a specific set of laboratory factors

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

Values Methodsa Row sample position Batch Chip position Totalb
β values Raw 11.4 9.5 6.5 30.4
Residuals 0.2 1.3 5.9 17.9
ComBat 0.2 1.3 6.0 17.1
SVA 0.6 1.3 0.9 6.5
M values Raw 12.3 9.7 6.8 30.7
Residuals 0.2 1.2 5.8 16.5
ComBat 0.2 1.3 6.2 17.0
SVA 0.4 0.7 0.8 5.3
  1. aResiduals, COMBAT and SVA methods used to correct effect due to batch and row sample position (within the chips)
  2. bTotal variability explained by laboratory factors and characteristics of the samples (recruitment centre, the five percentages of leukocyte subtypes, alcohol consumption, age and BMI, menopausal status, smoking, BC status and dietary folate)