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).

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.