runPreprocessing {compdiagTools}R Documentation

Pre-processing of an Affymetrix Dataset

Description

This function preprocesses a batch of Affymetrix .CEL-files. I.e., it checks the directory-structure, runs normalization and summary-statistics, produces diagnostic plots, and performs an Affymetrix-like quality control.

Usage

runPreprocessing(BASEPATH, COVDESC = paste(BASEPATH, "celfiles.lst", sep="/"), 
                 TMPPATH = "/scratch/local", 
                 EXPRSET = paste(BASEPATH, "expression_set.rdat", sep="/"), 
                 METHOD = "rma", plot.preprocessing = TRUE, run.simpleaffy = TRUE,
                 cleanup.plmsets = TRUE)

Arguments

BASEPATH Project path
COVDESC Path to text-file containing complete paths to Affymetrix .CEL-files, names of samples and optional covariates
TMPPATH Path to temporary directory for buffering AffyBatch-class with raw-data in it(default=/scratch/local/).
EXPRSET where to write the expression set containing the preprocessed data and corresponding documentation.
METHOD Method to be used for probeset summary ("rma" for medianpolish (default), other for affyPLM-method)
plot.preprocessing Logical value if quality-plots should be prepared
run.simpleaffy Logical value if Affymetrix MAS5-quality-assessment should be performed (qc)
cleanup.plmsets logical, TRUE if huge temporary data files are to be removed

Details

Under preparation

Value

Logical value if preprocessing finished correctely

Author(s)

Stefan Bentink

References

under preparation

See Also

PLMset-class, AffyBatch-class, qc


[Package compdiagTools version 1.5.3 Index]