qvalue

Q-value estimation for false discovery rate control

Bioconductor version: 2.8

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 <adabney at u.washington.edu> and John D. Storey <jstorey at u.washington.edu>, with assistance from Gregory R. Warnes <gregory_r_warnes at groton.pfizer.com>

Maintainer: John D. Storey <jstorey at u.washington.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 manual.pdf
PDF pHist.pdf
PDF qHist.pdf
PDF qPlots.pdf
PDF R Script qvalue Tutorial
PDF qvalue-002.pdf
PDF qvalue-004.pdf
PDF qvalue-006.pdf
PDF   Reference Manual

Details

biocViews MultipleComparisons
Depends
Imports graphics, grDevices, stats, tcltk
Suggests
System Requirements
License LGPL
URL
Depends On Me anota, DEGseq, gaia, PatientGeneSets, SSPA, webbioc
Imports Me anota, clusterProfiler, RNAinteract, webbioc
Suggests Me LBE, maanova
Version 1.26.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source qvalue_1.26.0.tar.gz
Windows Binary qvalue_1.26.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary qvalue_1.26.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center