The PaGE algorithm relies on some statistic to measure differential expression. In theory any statistic can be used and the confidence of the results will still accurate. However an unwise choise of statistic may have zero power for detecting differential expression.
PaGE 5.0 offers two statistics, the ratio of the means in the two groups, and the t-statistic.
Direct Design and Paired vs. Unpaired In the unpaired case the ratio of the means in the two groups is used. In the paired case and in the direct comparison design case the geometric mean of the ratios of the paired values is used. For more details, including precise definitions of these statistics, see the technical manual.