aroma.affymetrix (version 3.0.0)

NormExpBackgroundCorrection: The NormExpBackgroundCorrection class

Description

Package: aroma.affymetrix Class NormExpBackgroundCorrection

Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--BackgroundCorrection ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--LimmaBackgroundCorrection ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NormExpBackgroundCorrection

Directly known subclasses:

public static class NormExpBackgroundCorrection extends LimmaBackgroundCorrection

This class represents the normal exponential background correction model. Estimators of the limma package is used.

Usage

NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))

Arguments

...

Arguments passed to the constructor of LimmaBackgroundCorrection.

method

The estimator used, cf. argument normexp.method of backgroundCorrect in limma for more details.

Fields and Methods

Methods: No methods defined. Methods inherited from LimmaBackgroundCorrection: getAsteriskTags, getParameters, process 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

See Also

Internally, backgroundCorrect is used.