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Table 2 Batch-effect susceptible and erroneously corrected probes across datasets

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

Set Total probes Number of datasets considered as batch-effect susceptible, total and percentage
n 0 1 2 3 4 5
Batch-effect susceptible
All common probes 427,160 197,479 (46.2) 121,657 (28.5) 65,881 (15.4) 27,049 (6.3) 10,445 (2.4) 4649 (1.1)
Cross-hybridising 26,796 7446 (27.8) 5761 (21.5) 4692 (17.5) 3956 (14.8) 3097 (11.6) 1844 (6.9)
Multi-mappers 30,543 9092 (29.8) 6947 (22.7) 5575 (18.3) 4253 (13.9) 3032 (9.9) 1644 (5.4)
Type I 117,436 65,934 (56.1) 27,564 (23.5) 12,228 (10.4) 6445 (5.5) 3517 (3) 1748 (1.5)
Type I (≤ 2 internal CpG) 31,528 13,656 (43.3) 8528 (27) 4518 (14.3) 2779 (8.8) 1449 (4.6) 598 (1.9)
Type II 309,724 131,545 (42.5) 94,093 (30.4) 53,653 (17.3) 20,604 (6.7) 6928 (2.2) 2901 (0.9)
Type II (0 internal CpG) 131,010 43,578 (33.3) 42,855 (32.7) 27,389 (20.9) 11,862 (9.1) 3785 (2.9) 1541 (1.2)
Tm < 70 °C 7961 671 (8.4) 1426 (17.9) 2214 (27.8) 2424 (30.4) 1095 (13.8) 131 (1.6)
Erroneously corrected
All common probes 427,160 418,405 (98.0) 8755 (2.0) 5202 (1.2) 2860 (0.7) 1620 (0.4) 856 (0.2)