Automated Affymetrix Array Analysis Base Package

a4palette | Utility function that defines a color palette for use in a4 |

addQuantilesColors | Compute quantiles for plotGeneDE function |

boxPlot | Create a boxplot for a given gene. |

combineTwoExpressionSet | Combine two ExpressionSet objects |

computeLogRatio | Summary statistics for gene expression |

createExpressionSet | combine gene expression and phenotype data onto a... |

ExpressionSetWithComputation | Class "ExpressionSetWithComputation" |

filterVarInt | Filter Features On Intensity and Variance |

heatmap.expressionSet | Image plot of an expressionSet |

histPvalue | Plot the Distribution of P Values |

histpvalueplotter | Workhorse function for the histPvalue function |

lassoReg | Multiple regression using the Lasso algorithm as implemented... |

limmaTwoLevels | Wrapper function for the comparison of two groups using limma |

logReg | Logistic regression for predicting the probability to belong... |

nlcvTT | Data to Demonstrate nlcv and Co Functions |

plot1gene | Create a Profile Plot for a given Gene |

plotComb2Samples | Plots the correlation in gene expression between two samples |

plotCombination2genes | Plot a Combination of Two Genes |

plotCombMultSamples | Plots the correlation in gene expression between more than 2... |

plotLogRatio | Plot a summary gene expression graph |

probabilitiesPlot | Function to plot the probabilities to belong to a certain... |

probe2gene | Translate Affymetrix probeset IDs into gene symbols |

profilesPlot | Plot expression profiles of multiple genes or probesets |

propDEgenes | Generic function to compute the proportion of differentially... |

propdegenescalculation | Estimation of proportion of differentially expressed genes |

propDEgenes-methods | Methods for propDEgenes |

replicates | computes replicates across a vector |

spectralMap | Draw a Spectral Map |

spectralMap-methods | Methods for Function spectralMap |

topTable-methods | Methods for topTable |

tTest | Use t Test to Compare Two Groups |

volcanoPlot | Draw a Volcano Plot |

volcanoPlot-methods | Draw a Volcano Plot |

volcanoplotter | Workhorse function for the different volcanoPlot methods |

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