Extraction of Differential Gene Expression

apply_jackstraw | Non-Parametric Jackstraw for Principal Component Analysis... |

apply_qvalue | Estimate the q-values for a given set of p-values |

apply_snm | Supervised normalization of data in edge |

apply_sva | Estimate surrogate variables |

betaCoef | Regression coefficients from full model fit |

build_models | Generate a deSet object with full and null models |

build_study | Formulates the experimental models |

deFit-class | The differential expression class for the model fits |

deSet | Create a deSet object from an ExpressionSet |

deSet-class | The differential expression class (deSet) |

edge | Extraction of Differential Gene Expression |

endotoxin | Gene expression dataset from Calvano et al. (2005) Nature |

fitFull | Fitted data from the full model |

fit_models | Linear regression of the null and full models |

fitNull | Fitted data from the null model |

fullMatrix | Matrix representation of full model |

fullModel | Full model equation |

gibson | Gene expression dataset from Idaghdour et al. (2008) |

individual | Individuals sampled in experiment |

kidney | Gene expression dataset from Rodwell et al. (2004) |

kl_clust | Modular optimal discovery procedure (mODP) |

lrt | Performs F-test (likelihood ratio test using Normal... |

nullMatrix | Matrix representation of null model |

nullModel | Null model equation from deSet object |

odp | The optimal discovery procedure |

qvalueObj | Access/set qvalue slot |

resFull | Residuals of full model fit |

resNull | Residuals of null model fit |

show | Show function for deFit and deSet |

sType | Statistic type used in analysis |

summary | Summary of deFit and deSet |

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