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

• Published in: Bioinformatics Vol. 25; no. 7; pp. 964 - 966
• Main Authors: Käll, Lukas, Storey, John D., Noble, William Stafford
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.04.2009; Oxford Publishing Limited (England)
• Subjects: Algorithms; Applications Note; Bioinformatics; Biological and medical sciences; Computational Biology - methods; DNA - genetics; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Oligonucleotide Array Sequence Analysis; Probability; Sequence Alignment - methods; Software; Error; Non parametric estimation; Error probability; Posterior probability
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp021

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 Contact: lukas.kall@cbr.su.se Supplementary information: Supplementary data are available at Bioinformatics online.