Registration Open for Bioc2024 July 24-26


Q-value estimation for false discovery rate control

Bioconductor version: Release (3.19)

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 [aut, cre], Andrew J. Bass [aut], Alan Dabney [aut], David Robinson [aut], Gregory Warnes [ctb]

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

Citation (from within R, enter citation("qvalue")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

qvalue Package PDF R Script
Reference Manual PDF


biocViews MultipleComparisons, Software
Version 2.36.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License LGPL
Depends R (>= 2.10)
Imports splines, ggplot2, grid, reshape2
System Requirements
See More
Suggests knitr
Linking To
Depends On Me anota, DEGseq, DrugVsDisease, r3Cseq, webbioc, BonEV, cp4p, isva, ReAD, STAREG
Imports Me Anaquin, anota, clusterProfiler, CTSV, derfinder, DOSE, edge, erccdashboard, EventPointer, FindIT2, fishpond, metaseqR2, methylKit, MOMA, msmsTests, MWASTools, netresponse, normr, OPWeight, PAST, RiboDiPA, RNAsense, Rnits, RolDE, SDAMS, sights, signatureSearch, SpaceMarkers, subSeq, synapter, trigger, vsclust, webbioc, IHWpaper, AEenrich, cancerGI, fdrDiscreteNull, glmmSeq, groupedSurv, HDMT, jaccard, jackstraw, medScan, MetAlyzer, MOCHA, NBPSeq, qch, SeqFeatR, shinyExprPortal, ssizeRNA, TFactSR
Suggests Me biobroom, LBE, PREDA, RnBeads, swfdr, RNAinteractMAPK, BootstrapQTL, CpGassoc, dartR, dartR.base, dartR.popgen, DGEobj.utils, easylabel, familiar, mutoss, Rediscover, seqgendiff, volcano3D, wrMisc
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package qvalue_2.36.0.tar.gz
Windows Binary
macOS Binary (x86_64) qvalue_2.36.0.tgz
macOS Binary (arm64) qvalue_2.36.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats