Functions useful for those doing repetitive analyses with Affymetrix GeneChips.


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Documentation for package ‘affycoretools’ version 1.30.0

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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