To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

qvalue

 

Q-value estimation for false discovery rate control

Bioconductor version: Release (3.1)

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 Storey [aut, cre], Andrew Bass [ctb], Alan Dabney [ctb], David Robinson [ctb]

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

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("qvalue")

 

PDF R Script qvalue Package
PDF   Reference Manual
Text   NEWS

Details

biocViews MultipleComparisons, Software
Version 2.0.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10 years)
License LGPL
Depends R (>= 2.10)
Imports splines, ggplot2, grid, reshape2
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL http://qvalue.princeton.edu/ http://github.com/jdstorey/qvalue
Depends On Me anota, CancerMutationAnalysis, ChimpHumanBrainData, DEGseq, DrugVsDisease, metaseqR, prot2D, r3Cseq, SSPA, webbioc
Imports Me anota, clusterProfiler, derfinder, DOSE, edge, EnrichmentBrowser, erccdashboard, msmsTests, netresponse, Rnits, sRAP, synapter, trigger, webbioc
Suggests Me LBE, maanova, PREDA, RNAinteractMAPK
Build Report  

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Package Source qvalue_2.0.0.tar.gz
Windows Binary qvalue_2.0.0.zip
Mac OS X 10.6 (Snow Leopard) qvalue_2.0.0.tgz
Mac OS X 10.9 (Mavericks) qvalue_2.0.0.tgz
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