QVALITY: Non-parametric estimation of q-values and posterior error probabilities


QVALITY is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q-values, QVALITY employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution; for PEP estimation, QVALITY relies upon non-parametric logistic regression. Relative to other tools for estimating statistical confidence measures, QVALITY is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p-values.

Bioinformatics, 25 (7): 964–966