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 5.1 offers two statistics, the t-statistic and the ratio of the averages of the two groups (see --means).
Use this command to tell PaGE to use the t-statistic.
Direct Design and Paired vs. Unpaired In the unpaired case the 2-sample t-statistic is used. In the paired case and in the direct comparison design case the 1-sample t-statistic is used. For more details, including precise definitions of these statistics, see the technical manual.
The Tuning Parameter: Different statistics are sensitive to different kinds of false positives and false negatives. The t-statistic is very sensitive to the incidentally small variances that occur when there are relatively few replicates. The degree of this sensitivity can be controlled with the a tuning parameter added to the denominator of the t-stat formula. As a rule the power of the results goes up as this parameter goes up from zero, and it goes down as it increases without bound. Maximum power occurs with some moderate value of this parameter. PaGE sets this parameter for you automatically, as twice the mean value of the unadjusted denominator. This moderate value gives good general performance. You can override this default value using the --tstat_tuning_parameter command. For more on this parameter, see the technical manual.
This command takes no arguments.
> perl PaGE_5.1.6.pl --tstat