Estimation of local false discovery rate // 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.