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This is the development version of qvalue; for the stable release version, see qvalue.

Q-value estimation for false discovery rate control

Bioconductor version: Development (3.3)

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Author: John D. Storey with contributions from Andrew J. Bass, Alan Dabney and David Robinson

Maintainer: John D. Storey <jstorey at>, Andrew J. Bass <ajbass at>

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biocViews MultipleComparisons, Software
Version 2.3.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License LGPL
Depends R (>= 2.10)
Imports splines, ggplot2, grid, reshape2
Suggests knitr
Depends On Me anota, CancerMutationAnalysis, ChimpHumanBrainData, DEGseq, DrugVsDisease, metaseqR, prot2D, r3Cseq, SSPA, webbioc
Imports Me anota, clusterProfiler, derfinder, DOSE, edge, erccdashboard, msmsTests, netresponse, Rnits, sRAP, subSeq, synapter, trigger, webbioc
Suggests Me biobroom, LBE, maanova, PREDA, RNAinteractMAPK
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