Table 1 Beta differences after batch-effect removal across and datasets and preprocessing methods
Dataset | Method | Maximal probe-wise β difference | Groups (%) | ||||
|---|---|---|---|---|---|---|---|
Correction | Normalisation | Mean | Median | Low | Moderate | High | |
EpiSCOPE (450K) | Harman | Raw | 0.074 | 0.062 | 0.1 | 80.4 | 19.5 |
Illumina | 0.074 | 0.055 | 0.0 | 81.8 | 18.1 | ||
noob | 0.065 | 0.045 | 7.3 | 75.1 | 17.6 | ||
SWAN | 0.064 | 0.046 | 0.1 | 85.0 | 14.9 | ||
noob + SWAN | 0.061 | 0.040 | 8.4 | 75.4 | 16.1 | ||
Functional | 0.063 | 0.044 | 7.1 | 77.1 | 15.8 | ||
BMIQ | 0.073 | 0.062 | 0.1 | 80.8 | 19.2 | ||
noob + BMIQ | 0.072 | 0.050 | 10.3 | 66.8 | 22.9 | ||
ENmix | 0.067 | 0.041 | 8.0 | 73.1 | 18.9 | ||
ENmix-Quantile | 0.059 | 0.038 | 16.6 | 68.8 | 14.7 | ||
Dasen | 0.052 | 0.040 | 3.0 | 88.0 | 9.0 | ||
noob + Dasen | 0.055 | 0.038 | 14.0 | 73.2 | 12.8 | ||
ComBat | Raw | 0.100 | 0.079 | 0.2 | 63.9 | 35.9 | |
Illumina | 0.100 | 0.069 | 0.2 | 68.1 | 31.8 | ||
noob | 0.100 | 0.065 | 6.1 | 60.4 | 33.6 | ||
SWAN | 0.096 | 0.066 | 0.1 | 69.2 | 30.7 | ||
noob + SWAN | 0.099 | 0.061 | 5.9 | 61.5 | 32.7 | ||
Functional | 0.101 | 0.066 | 4.8 | 62.9 | 32.4 | ||
BMIQ | 0.102 | 0.082 | 0.2 | 62.9 | 36.9 | ||
noob + BMIQ | 0.101 | 0.060 | 9.5 | 57.8 | 32.7 | ||
ENmix | 0.105 | 0.064 | 8.1 | 58.2 | 33.7 | ||
ENmix-Quantile | 0.094 | 0.052 | 12.8 | 60.2 | 26.9 | ||
Dasen | 0.083 | 0.055 | 0.9 | 76.0 | 23.1 | ||
noob + Dasen | 0.090 | 0.054 | 8.0 | 64.9 | 27.1 | ||
BFiN (EPIC) | Harman | Raw | 0.065 | 0.060 | 1.8 | 71.6 | 26.6 |
Illumina | 0.053 | 0.038 | 5.0 | 75.6 | 19.4 | ||
noob | 0.049 | 0.034 | 18.6 | 61.2 | 20.2 | ||
SWAN | 0.052 | 0.042 | 1.3 | 83.8 | 14.9 | ||
noob + SWAN | 0.050 | 0.037 | 20.5 | 58.5 | 21.1 | ||
Functional | 0.051 | 0.036 | 17.8 | 60.3 | 21.9 | ||
BMIQ | 0.066 | 0.061 | 1.9 | 71.2 | 26.9 | ||
noob + BMIQ | 0.055 | 0.038 | 21.3 | 51.5 | 27.2 | ||
ENmix | 0.055 | 0.037 | 24.4 | 48.5 | 27.1 | ||
ENmix-Quantile | 0.050 | 0.033 | 31.1 | 47.5 | 21.5 | ||
Dasen | 0.041 | 0.033 | 14.7 | 78.1 | 7.2 | ||
noob + Dasen | 0.045 | 0.032 | 30.1 | 53.9 | 15.9 | ||
ComBat | Raw | 0.072 | 0.062 | 2.3 | 67.5 | 30.2 | |
Illumina | 0.056 | 0.039 | 7.3 | 73.4 | 19.3 | ||
noob | 0.058 | 0.038 | 14.2 | 62.3 | 23.5 | ||
SWAN | 0.059 | 0.044 | 1.9 | 79.0 | 19.2 | ||
noob + SWAN | 0.058 | 0.039 | 16.6 | 59.8 | 23.7 | ||
Functional | 0.060 | 0.040 | 13.7 | 61.0 | 25.3 | ||
BMIQ | 0.081 | 0.077 | 2.2 | 62.5 | 35.3 | ||
noob + BMIQ | 0.062 | 0.040 | 19.1 | 52.7 | 28.2 | ||
ENmix | 0.062 | 0.039 | 22.3 | 49.4 | 28.4 | ||
ENmix-Quantile | 0.058 | 0.036 | 25.7 | 48.7 | 25.6 | ||
Dasen | 0.050 | 0.036 | 12.0 | 73.6 | 14.4 | ||
noob + Dasen | 0.055 | 0.036 | 21.8 | 56.3 | 21.9 | ||