Reproducibility
| Correlation coefficient | False positives | |
| Wafer | ||
| cRNA Mix | 0.993 | 0 |
| CAOV-3 | 0.995 | 10 |
| Individual chips | ||
| cRNA Mix | 0.989 | 5 |
| CAOV-3 | 0.994 | 16 |
| Wafer vs. Indiv. chips | ||
| cRNA Mix | 0.982 | 19 |
| CAOV-3 | 0.980 | 31 |
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↵Each row corresponds to a comparison of identical samples hybridized to two separate arrays.
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↵The number of genes scored as present on at least one of the two arrays and differentially expressed (called as ‘increased’, ‘maybe increased’, ‘decreased’, ‘maybe decreased’ by theGeneChip software) by at least 1.8-fold with a change in signal intensity of at least 50 fluorescence units (a signal of 200 generally corresponds to ∼3–5 copies per mammalian cell [Lockhart and Winzeler 2000]). The total number of genes queried by the chips is ∼6800. The false positives shown here are for single comparisons. Because false positives are largely random, their numbers can be greatly minimized even further by performing replicate comparisons, as shown previously (Lockhart and Winzeler 2000; Sandberg et al. 2000).
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↵A pool of RNA from MCF-7 and T47D breast cancer cells and LnCap prostate cancer cells.
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↵CAOV-3 is a cell line derived from a malignant ovarian cancer.
