NormExpBackgroundCorrection: The NormExpBackgroundCorrection class

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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, names, objectSize, print, save, asThis

Author(s)

Henrik Bengtsson

See Also

Internally, backgroundCorrect is used.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.