chooseBestArray: Step 4: Where multiple arrays are present for some samples,...
In NeilPearson-Lilly/MethyLiution: MethyLiution: A QC Pipeline For Methylation Data

This probably isn't something you want to run directly. Just use the runPipeline() function.

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chooseBestArray(begin, mset_file, logfile, max_pval, max_prop,
  detection_freq_infofile, detection_filter_infofile, outdir,
  col.name = NULL, mset.lumi = NULL)

`begin`	Step the pipeline begins at
`mset_file`	Path to file in which dataset object is stored between steps (auto-filled by runPipeline() function)
`logfile`	Path to log file (auto-filled by runPipeline() function)
`max_pval`	Upper threshold for considering a result significant
`max_prop`	For each probe, the freq/proportion of assays that fail by max_pval of detection
`detection_freq_infofile`	Duplicated assays output file (auto-filled by runPipeline() function)
`detection_filter_infofile`	Detection failure table by probe file (auto-filled by runPipeline() function)
`outdir`	Path to output directory
`col.name`	List of column names, generated by setColumnNames() (auto-filled by runPipeline() function)
`mset.lumi`	Microarray dataset object (auto-filled by runPipeline() function)