PaGE 5.0 Documentation - the "level confidence" parameter

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 truly up, and 100(1-x)% to be false-positives. (Similarly for the negative levels and down-regulation.)

A confidence of 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.

The level confidence is a number between 0 and 1 (in the case of one non-reference condition), or a comma separated list of numbers between 0 and 1 (in the case of more than one non-reference condition).

User Strategy. The lower you set the level confidence, the more genes will be predicted and more levels will be generated. The trick is to find a level confidence that gives a "reasonable" amount of genes.
The Meaning of the Levels: Levels are generated as follows: If the statistic used is the t-statistic, a value of C is found so that the set of all genes with t-statistic greater than C is expected to have 100x% true positives and (1-x)100% false positives. Anything with statistic between 0 and C is given level 0, anything with statistic between C and 2C is given level 1, anything with statistic between 2C and 3C is given level 2. Etc. Negative levels are generated similarly. This is how PaGE generates patterns across conditions.
Gene Confidences: For each cutoff C there is a resultant set of predictions and a confidence for that set. Confidences are also applied to the individual gene as follows: Each cutoff C has a corresponding confidence. If the up-regulated gene has statistic S, then it is given the maximum confidence for all cutoffs C>S. Similarly for down-regulated. These are the confidences given in the PaGE report.

Note: If you have more than two conditions then you must specify a level confidence for each non-reference condition, as a comma separated list. For example if there are four conditions, c0, c1, c2, c3, then there are three confidences, and for example .75,.8,.65 would set them to .75, .8, and .65 respectively. The comma separated list must not have whitespace.

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