Functions useful for those doing repetitive analyses with Affymetrix GeneChips

affycoretools | Make repetitive analyses of microarray and RNA-Seq data... |

affycoretools-defunct | Defunct functions in package 'affycoretools' |

affystart | Pre-processing for Affymetrix Data |

annotateEset | Method to annotate ExpressionSets automatically |

dataAndHeatmapPage | A function to create an annotated HTML table for all genes in... |

entrezLinks | Add links to data when using ReportingTools |

fixHeaderAndGo | Fix data.frame header for use with ReportingTools |

geneSetPage | A function to create an HTML page for each gene set, as well... |

getCols | Correct Ordering of Contrasts |

getMainProbes | Remove control probesets from ST arrays |

gsHeatmap | A function to create a simple heatmap and key. |

intNames | Create Names for Venn Diagram Intersections |

make.cl | A Function to Make a Classlabel Vector for Plotting |

makeGoGeneTable | Make Gene table from GO analysis results |

makeGoTable | Create HTML tables for Gene Ontology (GO) analyses |

makeHmap | A function to create a heatmap-like object or matrix of... |

makeImages | Add dotplot images |

makeIndices | Create Indices for Venn Diagrams |

makeVenn | High-level function for making Venn diagrams and outputting... |

maplot | A Function to make MA plots from all arrays. |

mirna2mrna | A function to map miRNA to mRNA. |

outputRomer | A function to create HTML output from the results of running... |

pca.legend | A Function to Automagically Place a Legend in a PCA Plot |

plotDeg | Functions to Plot Density and RNA Degradation Plots |

plotPCA | A Function to Make a PCA Plot from an ExpressionSet or matrix |

runRomer | A function to run the romer function on a set of contrasts. |

tableFilt | Filter a topTable object |

venn4Way | 4-way Venn Diagrams |

vennCounts2 | Compute Counts for Venn Diagram |

vennPage | High-level function for making Venn diagrams with clickable... |

vennSelect2 | Select and Output Genelists Based on Venn Diagrams |

writeFit | Function to output annotated fit data from limma |

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