qvalue

Q-value estimation for false discovery rate control

Bioconductor version: Release (2.14)

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-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. 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: Alan Dabney and John D. Storey <jstorey at princeton.edu>

Maintainer: John D. Storey <jstorey at princeton.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("qvalue")

To cite this package in a publication, start R and enter:

    citation("qvalue")

Documentation

PDF R Script qvalue Tutorial
PDF   Reference Manual

Details

biocViews MultipleComparison, Software
Version 1.38.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License LGPL
Depends
Imports graphics, grDevices, stats, tcltk
Suggests
System Requirements
URL
Depends On Me anota, CancerMutationAnalysis, ChimpHumanBrainData, DEGseq, DrugVsDisease, metaseqR, netresponse, prot2D, r3Cseq, SSPA, webbioc
Imports Me anota, DOSE, msmsTests, ReactomePA, sRAP, synapter, trigger, webbioc
Suggests Me LBE, maanova, PREDA, RNAinteractMAPK

Package Downloads

Package Source qvalue_1.38.0.tar.gz
Windows Binary qvalue_1.38.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) qvalue_1.38.0.tgz
Mac OS X 10.9 (Mavericks)
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