Table 2.
Number of significant findings (p < 0.05) by microarray platform according to nominal p value, Bonferroni corrected p value, and FDR step-up corrected p value
| Overall treatment | OLZ vs. VEH | PCP vs. VEH | PCP vs. PCP + OLZ | |
|---|---|---|---|---|
| HG6800 | ||||
| Nominal p value | 1,952/1,897 | 198/190 (11↓, 187↑) | 2,504/2,425 (2,502↓, 2↑) | 1,796/1,735 (1,792↓, 4↑) |
| Bonferroni | 54/53 | 3/3 (0↓, 3↑) | 19/19 (19↓, 0↑) | 18/18 (18↓, 0↑) |
| Step-up | 801/785 | 5/5 (0↓, 5↑) | 1,216/1,191 (1,215↓, 1↑) | 295/288 (295↓, 0↑) |
| HG-U95 | ||||
| Nominal p value | 400/361 | 48/45 (19↓, 29↑) | 228/216 (215↓,13↑) | 166/156 (129↓, 37↑) |
| Bonferroni | 2/2 | 0 (0↓, 0↑) | 0 (0↓, 0↑) | 1 (1↓, 0↑) |
| Step-up | 13/13 | 0 (0↓, 0↑) | 0 (0↓, 0↑) | 1 (1↓, 0↑) |
| Overlap | ||||
| Nominal p value | 244 | 12 (0↓, 12↑) | 146 (145↓,1↑) | 85 (84↓, 1↑) |
| Bonferroni | 2 | 0 (0↓, 0↑) | 0 (0↓, 0↑) | 1 (1↓, 0↑) |
| Step-up | 8 | 0 (0↓, 0↑) | 0 (0↓, 0↑) | 1 (1↓, 0↑) |
The number of probesets/gene symbols is shown for each array. The overlap between both platforms is shown for the same comparisons in the last rows.