Table 1.
Observed and expected ranks. Observed and expected ranks from the Latin Square dataset for each of the four comparative methods, with linear correlation (R2) of MAS5 intensity vs concentration as quality control data.
| Chip | 92562 (R2 = 0.042) | 92563 (R2 = 0.123) | ||||||||
| Probe Set | Rank | Observed Rank | Rank | Observed Rank | ||||||
| S-Score | RMA | dChip | MAS5 | S-Score | RMA | dChip | MAS5 | |||
| BioB-5 | 4 | 5042 | 7182 | 88 | 491 | 7 | 11826 | 9395 | 125 | 539 |
| BioB-M | 8 | 20 | 5898 | 93 | 516 | 8 | 9 | 11023 | 136 | 61 |
| BioB-3 | 7 | 1966 | 3490 | 74 | 516 | 9 | 7 | 11810 | 145 | 3 |
| BioC-5 | 9 | 391 | 1336 | 53 | 110 | 1 | 3 | 2 | 2 | 1 |
| BioC-3 | 1 | 5 | 5 | 11 | 1 | 2 | 4 | 3 | 4 | 1 |
| BioDn-3 | 6 | 1 | 3 | 5 | 1 | 9 | 5 | 12560 | 179 | 1 |
| DapX-5 | 9 | 9652 | 1526 | 57 | 450 | 4 | 2 | 4 | 3 | 1 |
| DapX-M | 6 | 3 | 1 | 1 | 1 | 9 | 64 | 9497 | 132 | 96 |
| DapX-3 | 5 | 2 | 2 | 2 | 1 | 6 | 6 | 12443 | 155 | 1 |
| CreX-5 | 2 | 7018 | 1795 | 66 | 372 | 3 | 1 | 1 | 1 | 1 |
| CreX-3 | 3 | 501 | 7575 | 95 | 516 | 5 | 1080 | 4811 | 92 | 251 |
| Chip | 92564 (R2 = 0.047) | 92558 (R2 = 0.234) | ||||||||
| Probe Set | Rank | Observed Rank | Rank | Observed Rank | ||||||
| S-Score | RMA | dChip | MAS5 | S-Score | RMA | dChip | MAS5 | |||
| BioB-5 | 8 | 9628 | 4393 | 96 | 513 | 6 | 8 | 8 | 8 | 1 |
| BioB-M | 10 | 5 | 213 | 147 | 1 | 2 | 3 | 3 | 2 | 1 |
| BioB-3 | 9 | 6 | 47 | 140 | 1 | 1 | 2 | 2 | 3 | 1 |
| BioC-5 | 4 | 2 | 12626 | 1 | 1 | 9 | 5 | 5 | 6 | 1 |
| BioC-3 | 5 | 4 | 2119 | 112 | 1 | 10 | 6 | 6 | 7 | 1 |
| BioDn-3 | 3 | 8 | 359 | 138 | 1 | 1 | 1 | 4 | 4 | 1 |
| DapX-5 | 2 | 1 | 12625 | 2 | 1 | 5 | 12 | 13 | 30 | 1 |
| DapX-M | 1 | 1656 | 7093 | 105 | 513 | 7 | 10 | 7 | 9 | 1 |
| DapX-3 | 6 | 3 | 1233 | 122 | 1 | 3 | 7 | 9 | 13 | 1 |
| CreX-5 | 1 | 7 | 320 | 145 | 1 | 8 | 4 | 1 | 1 | 1 |
| CreX-3 | 7 | 22 | 11569 | 51 | 16 | 4 | 9 | 11 | 18 | 1 |
| Chip | 92559 (R2 = 0.302) | 92560 (R2 = 0.745) | ||||||||
| Probe Set | Rank | Observed Rank | Rank | Observed Rank | ||||||
| S-Score | RMA | dChip | MAS5 | S-Score | RMA | dChip | MAS5 | |||
| BioB-5 | 6 | 10 | 8 | 9 | 1 | 2 | 5 | 4 | 4 | 1 |
| BioB-M | 3 | 1 | 3 | 3 | 1 | 7 | 9 | 189 | 74 | 1 |
| BioB-3 | 4 | 2 | 4 | 4 | 1 | 3 | 1 | 2 | 2 | 1 |
| BioC-5 | 8 | 5 | 6 | 7 | 1 | 6 | 4 | 5 | 5 | 1 |
| BioC-3 | 9 | 7 | 7 | 8 | 1 | 9 | 6 | 6 | 6 | 1 |
| BioDn-3 | 9 | 9 | 16 | 73 | 1 | 8 | 10 | 881 | 87 | 1 |
| DapX-5 | 7 | 4 | 2 | 2 | 1 | 6 | 3 | 3 | 3 | 1 |
| DapX-M | 5 | 6 | 5 | 6 | 1 | 4 | 265 | 7339 | 115 | 130 |
| DapX-3 | 1 | 11 | 12 | 17 | 1 | 1 | 7 | 7 | 9 | 1 |
| CreX-5 | 9 | 3 | 1 | 1 | 1 | 9 | 2 | 1 | 1 | 1 |
| CreX-3 | 2 | 8 | 9 | 11 | 1 | 5 | 670 | 2511 | 95 | 126 |
| Chip | 92554 (R2 = 0.874) | 92555 (R2 = 0.668) | ||||||||
| Probe Set | Rank | Observed Rank | Rank | Observed Rank | ||||||
| S-Score | RMA | dChip | MAS5 | S-Score | RMA | dChip | MAS5 | |||
| BioB-5 | 3 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 |
| BioB-M | 6 | 4 | 5 | 6 | 1 | 5 | 7 | 10 | 11 | 1 |
| BioB-3 | 5 | 3 | 3 | 4 | 1 | 4 | 5 | 6 | 6 | 1 |
| BioC-5 | 1 | 8 | 12 | 37 | 1 | 2 | 10 | 7 | 7 | 1 |
| BioC-3 | 2 | 7 | 8 | 9 | 1 | 3 | 11 | 8 | 8 | 1 |
| BioDn-3 | 7 | 6 | 14 | 27 | 1 | 1 | 1 | 3 | 2 | 1 |
| DapX-5 | 4 | 10 | 6 | 13 | 1 | 3 | 9 | 9835 | 127 | 1 |
| DapX-M | 4 | 2 | 2 | 2 | 1 | 2 | 3 | 2 | 3 | 1 |
| DapX-3 | 9 | 5 | 4 | 5 | 1 | 6 | 6 | 5 | 5 | 1 |
| CreX-5 | 4 | 11 | 7 | 14 | 1 | 6 | 4 | 4 | 4 | 1 |
| CreX-3 | 8 | 19 | 178 | 64 | 4 | 4 | 8 | 9089 | 122 | 1 |
| Chip | 92556 (R2 = 0.748) | 92557 (R2 = 0.756) | ||||||||
| Probe Set | Rank | Observed Rank | Rank | Observed Rank | ||||||
| S-Score | RMA | dChip | MAS5 | S-Score | RMA | dChip | MAS5 | |||
| BioB-5 | 1 | 3 | 1 | 1 | 1 | 1 | 2 | 2 | 2 | 1 |
| BioB-M | 3 | 2 | 3 | 2 | 1 | 4 | 4 | 3 | 1 | 1 |
| BioB-3 | 8 | 7 | 22 | 37 | 1 | 2 | 3 | 1 | 3 | 1 |
| BioC-5 | 4 | 9 | 19 | 29 | 1 | 3 | 14 | 373 | 54 | 1 |
| BioC-3 | 4 | 8 | 6 | 11 | 1 | 9 | 5 | 300 | 56 | 1 |
| BioDn-3 | 4 | 1 | 4 | 4 | 1 | 5 | 1 | 4 | 4 | 1 |
| DapX-5 | 8 | 6 | 8 | 9 | 1 | 10 | 9 | 9 | 10 | 1 |
| DapX-M | 2 | 4 | 2 | 3 | 1 | 11 | 10 | 87 | 78 | 1 |
| DapX-3 | 5 | 14 | 11 | 23 | 1 | 6 | 7 | 7596 | 107 | 1 |
| CreX-5 | 7 | 5 | 5 | 7 | 1 | 8 | 8 | 16 | 19 | 1 |
| CreX-3 | 6 | 10 | 7 | 12 | 1 | 7 | 6 | 1151 | 72 | 1 |