runCDNAPreprocessing {compdiagTools}R Documentation

Preprocessing of a CDNA Dataset

Description

This function processes a batch of xls-data files. It checks the directory-structure, runs normalization and summary-statistics, produces diagnostic plots, and performs a quality control.

Usage

runCDNAPreprocessing(BASEPATH, COVDESC = paste(BASEPATH, "celfiles.lst", sep = "/"), EXPRSET = paste(BASEPATH, "expression_set.rdat", sep = "/"), TMPPATH = "/scratch/local", METHOD = "loess", CHIP = "NA", plot.preprocessing = TRUE)

Arguments

BASEPATH The main path of the project.
COVDESC Path of the celfiles.lst file (containing the list od datafiles) of the project.
EXPRSET Path of the celfiles.lst file (containing the list od datafiles) of the project.
TMPPATH In this path the raw dataset will be stored temporaly (an additional timestamp will be addet to the path).
METHOD This string defines the used normalization method of th marray package ("loess", "median", "twoD"...(see maNorm()))
CHIP The filename of the userdefined layout, if a non standart layout is used.
plot.preprocessing Flags if plotting should be done or not.

Details

The function reads a bunch of unzipped or gzipped data named in the celfiles.lst file. The data is normalized whith the defined method (e.g. loess), imputed to fill up undefined values, afterwars vsn is performed. Some box- and mva plots are done and the resulting expression set is saved.

Value

Logical value if preprocessing finished correctely

Author(s)

Matthias Maneck

See Also

package for data imout and normalization, PLMset-class, AffyBatch-class, qc


[Package compdiagTools version 1.5.3 Index]