Table 1 Summary of the effect of mean batch-centering on data generated from different experiments.
Within two-fold consistent (%) | SAM Common, top 1000 | ||||||||
|---|---|---|---|---|---|---|---|---|---|
Data from different experiments | Probesets | Between datasets | Across datasets | Between datasets | Across datasets | ||||
Before | After | Before | After | Before | After | Before | After | ||
Amplified 10 ng and unamplified 10 μg protocols, RMA, U133A | 22283 | 20645 (92%) (Fig 1A) | 20645 (92%) (Fig 1A) | 13221 (59%) (Fig 1B) | 22283 (100%) (Fig 1B) | 522 (0.031) (0.032) | 522 (0.031) (0.032) | 251 (0.023) (0.037) | 594 (0.025) (0.035) |
U133A and plus 2.0 arrays common, MAS5 present = 4/6 chips | 11198 | 10641 (95%) | 10669 (95%) | 2675 (24%) | 11170 (100%) | 493 (0.037) (0.036) | 493 (0.037) (0.036) | 112 (0.026) (0.027) | 954 (0.041) (0.040) |
Exon v U133 plus 2 (consensus mapping) Plier and MAS5 | 44280 | 37255 (84%) | 37255 (84%) | 9485 (21%) | 44280 (100%) | 528 (0.067) (0.060) | 528 (0.067) (0.060) | 569 (0.024) (0.020) | 847 (0.110) (0.089) |
Exon v U133 plus 2 (SIF mapping) Plier and MAS5 | 13730 | 12028 (88%) | 12028 (88%) | 3626 (26%) | 13730 (100%) | 524 (0.068) (0.060) | 524 (0.068) (0.060) | 731 (0.026) (0.026) | 916 (0.569) (0.370) |
Standard 10 μg and revised 2 μg protocols, RMA, U133A | 22283 | 21303 (96%) | 21303 (96%) | 19779 (89%) | 22283 (100%) | 688 (0.035) (0.050) | 688 (0.035) (0.050) | 618 (0.039) (0.044) | 901 (0.044) (0.042) |
GeneChip 3000 and GeneArray 2500 scanners, RMA, U133A | 22283 | 22276 (100%) | 22276 (100%) | 22282 (100%) | 22283 (100%) | 883 (0) (0) | 883 (0) (0) | 872 (0) (0) | 879 (0) (0) |
NuGEN 10 ng and EpiStem 2 ng amplification, RMA, U133 plus 2 | 54675 | 49308 (90%) | 49308 (90%) | 28276 (52%) | 54675 (100%) | 530 (0.060) (0.066) | 530 (0.060) (0.066) | 364 (0.035) (0.034) | 743 (0.070) (0.069) |