XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

burnin | Indicator for running a MCMC burnin |

calculatePosteriorAvg | Calculate the posterior average for indicators of concordant... |

empiricalStart | Empirical starting values for the MCMC |

expressionSetList | Example of ExpressionSetList |

ExpressionSetList-class | A class for containing a list of ExpressionSets |

ExpressionSetList-methods | Methods for ExpressionSetList |

firstMcmc | Values for the first MCMC iteration |

geneCenter | Center the expression values for each gene in a study to zero |

hyperparameters | Accessor for hyperparameters of the Bayesian model |

iterations | Number of MCMC iterations |

lastMcmc | MCMC values for the last iteration |

output | Options for storing results of the MCMC chains |

pairs | pairs function for high-throughput data |

Parameters-class | Container for XDE parameters |

posteriorAvg | Accessor and replacement methods for posterior averages of... |

seed | Seed for the MCMC |

ssStatistic | Calculate single study estimates of effect size |

standardizeSamples | Centers the genes at zero and standardizes the samples to... |

studyCenter | Center the expression values in a study to zero |

symbolsInteresting | Useful for changing the look of pairs plots to emphasize... |

thin | How often to write MCMC iterations to file |

tuning | Tuning parameters for Metropolis-Hastings proposals |

updates | Frequency of updating a parameter per MCMC iteration |

xde | Fit the Bayesian hierarchical model for cross-study... |

XdeMcmc-class | Class for storing output from the Bayesian model |

XdeParameter-class | Container class for storing options of the Bayesian... |

xmcmc | Object of class XdeMcmc |

xsScores | Alternative cross-study scores of differential expression |

zeroNu | Option for not modeling Nu |

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