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.
From: Empirical validation of the S-Score algorithm in the analysis of gene expression 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 (R 2 = 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 (R 2 = 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 (R 2 = 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 (R 2 = 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 |