DOI: 10.18129/B9.bioc.qvalue  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see qvalue.

Q-value estimation for false discovery rate control

Bioconductor version: 3.16

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 princeton.edu>, Andrew J. Bass <ajbass at princeton.edu>

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biocViews MultipleComparisons, Software
Version 2.30.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License LGPL
Depends R (>= 2.10)
Imports splines, ggplot2, grid, reshape2
Suggests knitr
URL http://github.com/jdstorey/qvalue
Depends On Me anota, ChimpHumanBrainData, DEGseq, DrugVsDisease, r3Cseq, webbioc
Imports Me Anaquin, anota, anota2seq, ChAMP, clusterProfiler, CTSV, derfinder, DOSE, edge, epihet, erccdashboard, EventPointer, FindIT2, fishpond, IHWpaper, InTAD, metaseqR2, methylKit, MOMA, msmsTests, MWASTools, netresponse, normr, OPWeight, PAST, RiboDiPA, RNAsense, Rnits, RolDE, SDAMS, sights, signatureSearch, subSeq, synapter, trigger, vsclust, webbioc
Suggests Me biobroom, LBE, maanova, PREDA, RNAinteractMAPK, RnBeads, RnBeads, SummarizedBenchmark, swfdr
Links To Me
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