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