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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