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Table 1 Beta differences after batch-effect removal across and datasets and preprocessing methods

From: Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data

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