# Functions useful for those doing repetitive analyses with Affymetrix GeneChips.

## Documentation for package ‘affycoretools’ version 1.30.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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