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 pvalue level. The resulting curve of pvalues versus local false discovery rate offers an insight into the twilight zone between clear differential and clear nondifferential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a twocondition test on differences in means for a given input matrix or expression set and computes permutation based pvalues. 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.
Package details 


Author  Stefanie Scheid <[email protected]> 
Bioconductor views  DifferentialExpression Microarray MultipleComparison 
Maintainer  Stefanie Scheid <[email protected]> 
License  GPL (>= 2) 
Version  1.53.0 
URL  http://compdiag.molgen.mpg.de/software/twilight.shtml 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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