twilight

Estimation of local false discovery rate

Bioconductor version: 2.8

In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.

Author: Stefanie Scheid <stefanie.scheid at gmx.de>

Maintainer: Stefanie Scheid <stefanie.scheid at gmx.de>

To install this package, start R and enter:

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

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

    citation("twilight")

Documentation

PDF bcb_logo.pdf
PDF R Script Estimation of Local False Discovery Rates
PDF   Reference Manual

Details

biocViews Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons
Depends R (>= 2.1.0), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0)
Imports Biobase, graphics, grDevices, stats
Suggests golubEsets(>= 1.4.2), vsn(>= 1.7.2)
System Requirements
License GPL (>= 2)
URL http://compdiag.molgen.mpg.de/software/twilight.shtml
Depends On Me OrderedList
Imports Me OrderedList
Suggests Me
Version 1.28.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source twilight_1.28.0.tar.gz
Windows Binary twilight_1.28.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary twilight_1.28.0.tgz
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