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Bioinformatics. 2009 Apr 1;25(7):964-6. doi: 10.1093/bioinformatics/btp021. Epub 2009 Feb 4.

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

Author information

  • 1Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Sweden, USA. lukas.kall@cbr.su.se

Abstract

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.

AVAILABILITY:

A web server, C++ source code and binaries are available under MIT license at http://noble.gs.washington.edu/proj/qvality.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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