GcRmaBackgroundCorrection: The GcRmaBackgroundCorrection class

Description

Package: aroma.affymetrix Class GcRmaBackgroundCorrection

Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--BackgroundCorrection ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--GcRmaBackgroundCorrection

Directly known subclasses:

public static class GcRmaBackgroundCorrection extends BackgroundCorrection

This class represents the GCRMA background adjustment function.

Usage

GcRmaBackgroundCorrection(..., indicesNegativeControl=NULL, affinities=NULL, type=c("fullmodel", "affinities"), opticalAdjust=TRUE, gsbAdjust=TRUE, gsbParameters=NULL, seed=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

indicesNegativeControl

Locations of any negative control probes (e.g., the anti-genomic controls on the human exon array). If NULL and type == "affinities", then all non-PM probes are used as the negative controls.

affinities

A numeric vector of probe affinities, usually as calculated by computeAffinities() of the AffymetrixCdfFile class.

type

Type (flavor) of background correction, which can be either "fullmodel" (uses MMs; requires that the chip type has PM/MM pairs) or "affinities" (uses probe sequence only).

gsbAdjust

If TRUE, adjustment for specific binding is done, otherwise not.

opticalAdjust

If TRUE, correction for optical effect is done first, utilizing OpticalBackgroundCorrection.

gsbParameters

Additional argument passed to the internal bgAdjustGcrma() method.

seed

An (optional) integer specifying a temporary random seed to be used during processing. The random seed is set to its original state when done. If NULL, it is not set.

Fields and Methods

Methods:

	`process`
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Methods inherited from BackgroundCorrection: getParameters, process Methods inherited from ProbeLevelTransform: getRootPath Methods inherited from Transform: getOutputDataSet, getOutputFiles Methods inherited from AromaTransform: as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags Methods inherited from ParametersInterface: getParameterSets, getParameters, getParametersAsString Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

References

[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer. A Model Based Background Adjustment for Oligonucleotide Expression Arrays, JASA, 2004.