Functions useful for those doing repetitive analyses with Affymetrix GeneChips.


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Documentation for package ‘affycoretools’ version 1.32.1

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affystart Pre-processing for Affymetrix Data
annBM Select Available Annotation from a Biomart
dataAndHeatmapPage A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.
foldFilt Output Fold Change Data
foldFiltBM Output Fold Change Data using biomaRt
geneSetPage A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.
getMainProbes Remove control probesets from ST arrays
getUniqueLL Subset a Vector of Probesets
gsHeatmap A function to create a simple heatmap and key.
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.
makeVenn High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.
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 romer on a set of contrasts.
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
runRomer A function to run the romer function on a set of contrasts.
vennCounts2 Compute Counts for Venn Diagram
vennPage High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.
vennSelect Select and Output Genelists Based on Venn Diagrams
vennSelect2 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