Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

BMC Genomics

Table 3 False Positive Rates.

Method	Golden Spike	Gene Logic Tonsil	Affymetrix Latin Square
ANOVA	0.286 (0.135)	0.146 (0.007)	0.096 (0.018)
Combined P	0.374 (0.110)	0.146 (0.003)	0.155 (0.007)
Cyber-T	0.190 (0.096)	0.037 (0.005)	0.047 (0.017)
Median t	0.004 (0.131)	2.8 × 10^-4 (0.008)	2.8 × 10^-4 (0.023)
Moderated t	0.160 (0.079)	0.027 (0.006)	0.034 (0.014)
Original t	0.123 (0.051)	0.024 (0.007)	0.035 (0.016)

This table shows the observed false positive rate calculated using a p-value cutoff of 0.01. The false positive rate based on a calibrated p-value of 0.01 is shown in parentheses. The calibrated p-value was calculated using probe sets called Absent on all arrays for a given experiment. For the combined p method, a p-value cutoff of 0.005 was used because we use the minimum of the two one-sided combined p-values.

ISSN: 1471-2164