GcRmaBackgroundCorrection: The GcRmaBackgroundCorrection class

Description

Package: aroma.affymetrix Class GcRmaBackgroundCorrection Object ~~| ~~+--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="fullmodel", opticalAdjust=TRUE, gsbAdjust=TRUE, gsbParameters=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

indicesNegativeControl, affinities, type, opticalAdjust, gsbAdjust, gsbParameters

Additional arguments passed to the internal bgAdjustGcrma() method.

Fields and Methods

Methods: rll{ process Performs background correction. } Methods inherited from BackgroundCorrection: process Methods inherited from Transform: getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles Methods inherited from AromaTransform: getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags Methods inherited from Object: asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save