Functions useful for those doing repetitive analyses with Affymetrix GeneChips.

Documentation for package ‘affycoretools’ version 1.30.0

affystart	Pre-processing for Affymetrix Data
annBM	Select Available Annotation from a Biomart
foldFilt	Output Fold Change Data
foldFiltBM	Output Fold Change Data using biomaRt
getUniqueLL	Subset a Vector of Probesets
hyperG2annaffy	HTML tables from GOIDs
hyperGoutput	Output Tables Based on Hypergeometric Test
limma2annaffy	Function to Create HTML Tables from limma Objects
limma2annaffy.na	Function to Create HTML Tables from limma Objects
limma2biomaRt	Function to Create HTML Tables from limma Objects using biomaRt for Annotation
limma2biomaRt.na	Function to Create HTML Tables from limma Objects using biomaRt for Annotation
linksBM	Select Available Annotation from a Biomart
makeHmap	A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data.
maplot	A Function to make MA plots from all arrays.
mirna2mrna	A function to map miRNA to mRNA.
plotDeg	Functions to Plot Density and RNA Degradation Plots
plotHist	Functions to Plot Density and RNA Degradation Plots
plotPCA	A Function to Make a PCA Plot from an ExpressionSet
probes2table	Convert Affy Probe ids to Annotated HTML Table
probes2tableBM	Convert Affy Probe ids to Annotated HTML Table using biomaRt
vennCounts2	Compute Counts for Venn Diagram
vennSelect	Select and Output Genelists Based on Venn Diagrams
vennSelectBM	Select and Output Genelists Based on Venn Diagrams using biomaRt
vennSelectFC	Select and Output Gene Lists Based on Venn Diagrams
writeFit	Function to output annotated fit data from limma