# twilight v1.48.0

## 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.

## Functions in twilight

Name | Description | |

twilight.combi | All permutations of a binary vector | |

twilight.getlambda | Internal function to compute regularization parameter lambda | |

twilight | Estimation of the local false discovery rate | |

twilight.getmatrix | Internal function to extract the gene expression matrix from an expression set | |

expval | Example of twilight.pval result | |

twilight.permute.unpair | Permutation matrix of unpaired class labels | |

twilight.permute.pair | Permutation matrix of paired class labels | |

twilight.teststat | Interface to the test statistics provided within 'twilight' | |

print.twilight | Print function for twilight objects | |

exfdr | Example of twilight result | |

twilight.filtering | Permutation filtering | |

plot.twilight | Plot function for twilight objects | |

twilight.pval | Compute p-values from expression sets | |

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## Last year downloads

## Details

License | GPL (>= 2) |

URL | http://compdiag.molgen.mpg.de/software/twilight.shtml |

biocViews | Microarray, DifferentialExpression, MultipleComparison |

depends | base (>= 2.10) , Biobase (>= 1.12.0) , R (>= 2.10) , splines (>= 2.2.0) , stats (>= 2.2.0) |

suggests | golubEsets (>= 1.4.2) , vsn (>= 1.7.2) |

imports | graphics , grDevices |

Contributors | Stefanie Scheid |

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