This package takes a list of pvalues resulting from the simultaneous testing of many hypotheses and estimates their qvalues and local FDR values. The qvalue 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 pvalue. Various plots are automatically generated, allowing one to make sensible significance cutoffs. Several mathematical results have recently been shown on the conservative accuracy of the estimated qvalues from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.
Package details 


Author  John D. Storey with contributions from Andrew J. Bass, Alan Dabney and David Robinson 
Bioconductor views  MultipleComparisons 
Maintainer  John D. Storey <[email protected]>, Andrew J. Bass <[email protected]> 
License  LGPL 
Version  2.14.0 
URL  http://github.com/jdstorey/qvalue 
Package repository  View on Bioconductor 
Installation 
Install the latest version of this package by entering the following in R:

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