Read CEL files and perform FIRMA analysis

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Description

The function makes use of the aroma.affymetrix package to analyze Affymetrix Human Exon 1.0 ST Arrays. The function reads CEL files, and performs background correction, normalization (customized RMA approach), and alternative splicing analysis according to the FIRMA method (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis). The function returns a data.frame with log2 FIRMA (alternative splicing) scores for each probeset/sample combination.

Usage

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    firmaAnalysis(useToyData, aromaPath, dataSetName)

Arguments

useToyData

Boolean argument to indicate whether sample data sets included in the TIN package should be used in the analysis.

aromaPath

Absolute or relative path to the aroma.affymetrix directory. Requires custom CDF annotation file (please refer to the FIRMA vignette for download and setup).

dataSetName

Name of folder in the 'aromaPath' containing raw data (CEL files; please refer to the FIRMA vignette for setup).

Value

A data.frame with expression level values after the FIRMA analysis has been applied. The data.frame consists of one column for each sample and one row for each probeset.

References

E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed, FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics, 2008.

Examples

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# Perform FIRMA analysis on the raw expression data
# To use sample data sets included in the TIN package as input:
    fs <- firmaAnalysis(useToyData=TRUE)

# To use your own data, provide path to aroma.affymetrix root directory and
# name of data set as arguments:
#   fs <- firmaAnalysis(useToyData=FALSE, "/tmp/path/to/aroma.affymetrix",
#   "sampleSet")