Table 3.
Degree of probe set consolidation by the SCOREM algorithm in eight data sets
| Experiment | Probe sets (Genes)a |
Consolidation level (%) |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| On GeneChip® | After filtering | Unannotated | Single | Redundant | After SCOREM | None | Partial | Complete | |
| GSE3678 | 54 675 (19 798) | 18 725 (10 516) | 2578 | 6802 | 9345 (3714) | 6668 (3714) | 44 | 19 | 37 |
| GSE4051 | 45 101 (20 757) | 16 992 (9963) | 1996 | 6645 | 8351 (3318) | 5019 (3318) | 27 | 19 | 54 |
| GSE4799 | 45 101 (20 757) | 44 062 (20 459) | 6597 | 11 006 | 26 459 (9453) | 24 192 (9453) | 80 | 15 | 5 |
| GSE9371 | 45 101 (20 757) | 20 728 (11 184) | 1937 | 6512 | 12 279 (4672) | 9094 (4672) | 47 | 22 | 30 |
| BrCa | 22 283 (12 718) | 13 397 (8558) | 982 | 5939 | 6476 (2619) | 4031 (2619) | 28 | 19 | 53 |
| VSMC | 45 101 (20 757) | 19 914 (11 717) | 1012 | 7171 | 11 731 (4546) | 8224 (4546) | 44 | 19 | 37 |
| GonFat | 45 101 (20 757) | 24 260 (12 586) | 2472 | 7073 | 14 715 (5513) | 9320 (5513) | 30 | 23 | 48 |
| IngFat | 45 101 (20 757) | 24 364 (12 585) | 2590 | 7080 | 14 694 (5505) | 8966 (5505) | 28 | 20 | 52 |
aNumbers in parentheses indicate the number of distinct genes represented by those probe sets.