title: QVALITY: non-parametric estimation of q-values and posterior error probabilities.
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.
  
  
  BACKGROUND
  A web server, C++ source code and binaries are available under MIT license at http://noble.gs.washington.edu/proj/qvality.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Sweden, USA. lukas.kall@cbr.su.se
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
authors.forename: John D
authors.initials: JD
authors.lastname: Storey
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011336:Probability; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D004247:DNA