Methods for analyzing microarray data using Local Pooled Error (LPE) method

am.trans | Transform replicated arrays into (A,M) format |

baseOlig.error | Evaluates LPE variance function of M for quantiles of A... |

baseOlig.error.step1 | Evaluates LPE variance function of M for quantiles of A... |

baseOlig.error.step2 | Evaluates LPE variance function of M for quantiles of A... |

fdr.adjust | FDR adjustment procedures |

fixbounds.predict.smooth.spline | Makes the predicted variance non negative |

iqr | Inter-quartile range |

Ley | Gene Expression Data from Mouse Immune response study, (2002) |

lowess.normalize | lowess normalization of the data (based on M vs A graph) |

lpe | Evaluates local pooled error significance test |

mt.rawp2adjp | Adjusted p-values for simple multiple testing procedures |

n.genes.adaptive.int | Calcuates the number of genes in various intervals... |

permute | Calculating all possible permutations of a vector |

preprocess | Preprocessing the data (IQR normalization, thresholding, log-... |

quan.norm | Finding quartile range |

quartile.normalize | Normalization based on quartile range |

resamp.adj | Resampling based fdr adjustment |

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