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 Performs background correction.

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, names, objectSize, print, save, asThis

Author

Ken Simpson, Henrik Bengtsson

References

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