Starr: Simple Tiling ARRay analysis for Affymetrix ChIP-chip data
نویسندگان
چکیده
Starr is an extension of the Ringo [6] package for the analysis of ChIP-chip projects. Whereas the latter is specialized to the processing of Nimblegen and Agilent arrays, the former provides all corresponding features for Affymetrix arrays. Data can be read in from Affymetrix CEL-files, or from text files in gff format. Standard quality assessment and data normalization tools are available. Starr uses the Bioconductor ExpressionSet class for data storage. The probeAnno class from Ringo serves as a mapping of the ChIP signals onto the genomic position. Consequently, all functions from Ringo that operate on either ExpressinoSet or probeAnno can be used without modification. These include smoothing operations, peak-finding, and quality control plots. Starr adds new options for high-level analysis of ChIP-chip data. We demonstrate Starr’s facilities at the example of an experiment that compares DNA binding under two different conditions. Three chips have been produced, two contain the actual immunoprecipitated DNA, and the other one is a control experiment.
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