QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

boxPlots | Draw parallel plots for top results in whole-genome-wide... |

densityPlots | Draw estimated density plots for all arrays |

genExprSet | Generate an ExpressionSet object |

genSimData.BayesNormal | Generating simulated data set from conditional normal... |

getPCAFunc | Get principal components of arrays |

glmWrapper | Perform glm test for all gene probes |

lkhrWrapper | Perform glm test for all gene probes |

lmFitPaired | A wrapper function for the function 'lmFit' of the R... |

lmFitWrapper | A wrapper function for the function 'lmFit' of the R... |

LumiBatch2Table | Output slots (exprs, pData, fData) of an LumiBatch object... |

pca2DPlot | Scatter plot of first 2 principal components |

pca3DPlot | Scatter plot of 3 specified principal components |

plotCurves | Plot trajectories of probe profiles across arrays |

plotQCCurves | Plot trajectories of specific QC probes (e.g., biotin,... |

plotSamplep95p05 | Plot trajectories of the ratio of 95th percentile to 5th... |

quantilePlot | Plot trajectories of quantiles across arrays |

R2PlotFunc | Draw heatmap of square of correlations among arrays |

scatterPlots | Draw scatter plots for top results in whole-genome-wide... |

sortExpressionSet | Sort the order of samples for an ExpressionSet object |

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