The program tests microarray data for significance. It calculates p-values and adjusted p-values for every gene.
The procedure works as follows:
First, the logarithms of the ratios are calculated. The logarithms of the ratios follow a normal distribution. Then, a standard t-test is performed on the transformed values. This yields a confidence interval for the true value of the ratio and a p-value for every gene.
From the list of p-values adjusted p-values are calculated. The adjusted p-values give estimations for the false discovery rate and the family wise error rate.
The false discovery rate: Storey JD. (2002) A direct approach to false discovery rates.
Journal of the Royal Statistical Society, Series B, 64: 479-498
The more conservative false discovery rate, reported in the BH column of the results of the analysis:
Y. Benjamini and Y. Hochberg (1995).
Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B. Vol. 57: 289-300.