# FAMT v2.5

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## Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data

The method proposed in this package takes into account the impact of dependence on the multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered in the model is chosen to reduce the false discoveries variance in multiple tests. The model parameters are estimated thanks to an EM algorithm. Adjusted tests statistics are derived, as well as the associated p-values. The proportion of true null hypotheses (an important parameter when controlling the false discovery rate) is also estimated from the FAMT model. Graphics are proposed to interpret and describe the factors.

## Functions in FAMT

Name | Description | |

FAMT-package | Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data | |

raw.pvalues | Calculation of classical multiple testing statistics and p-values | |

covariates | Covariates data frame | |

annotations | Gene annotations data frame | |

as.FAMTdata | Create a 'FAMTdata' object from an expression, covariates and annotations dataset | |

emfa | Factor Analysis model adjustment with the EM algorithm | |

pi0FAMT | Estimation of the Proportion of True Null Hypotheses | |

nbfactors | Estimation of the optimal number of factors of the FA model | |

summaryFAMT | Summary of a FAMTdata or a FAMTmodel | |

defacto | FAMT factors description | |

modelFAMT | The FAMT complete multiple testing procedure | |

residualsFAMT | Calculation of residual under null hypothesis | |

expression | Gene expressions data frame | |

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## Details

Type | Package |

Date | 2013-09-30 |

LazyLoad | yes |

License | GPL (>= 2) |

URL | http://famt.free.fr/ |

Packaged | 2014-01-02 14:02:18 UTC; ripley |

NeedsCompilation | no |

Repository | CRAN |

Date/Publication | 2014-01-02 15:15:13 |

depends | impute , mnormt |

Contributors | Chloe Friguet, Maela Kloareg, David Causeur, Magalie Houee-Bigot |

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