PaGE_5.1 Documentation - the --level_confidence command

This is the most important parameter to use when running PaGE.

The level_confidence is a number between zero and one and gives the confidence at which the levels are generated. Positive levels in PaGE output indicate up-regulation from the reference condition (condition 0), while negative levels indicate down-regulation from the reference condition.

A level_confidence of x means that we expect 100x% of the set of all genes with positive levels to be truely up, and 100(1-x)% to be false-positives. (Similarly for the negative levels and down-regulation.)

Confidence x means that roughly 100x% of the predictions should be true. So for those familiar with the False Discovery Rate (FDR), the confidence x = 1 - FDR.

This command takes one argument of type float, which must be strictly between 0 and 1.

Note: If you have more than two conditions and you use --level_confidence then that confidence will be applied to all positions in the pattern. To apply a separate level_confidence to each position in the patterns use --level_confidence_list.

See the technical manual for more detailed information on how the confidence is determined.

Example:

> perl PaGE_5.1.6.pl --level_confidence .8