ExonRmaPlm: The ExonRmaPlm class

Description

Package: aroma.affymetrix
Class ExonRmaPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ExonRmaPlm

Directly known subclasses:

public abstract static class ExonRmaPlm
extends RmaPlm

This class represents the log-additive model part of the Robust Multichip Analysis (RMA) method described in Irizarry et al (2003), as implemented for exon arrays. The model may be fitted with exons merged into transcripts (all probes fitted together) or on an individual exon basis (probes within an exon treated as a group, but exons fitted separately).

Usage

ExonRmaPlm(..., mergeGroups=TRUE)

Arguments

...: Arguments passed to RmaPlm.
mergeGroups: A logical flag specifying whether to merge exons into transcripts.

Fields and Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getProbeAffinityFile`	-
	`setMergeGroups`	-

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, 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

Model

RmaPlm.

Author

Ken Simpson, Henrik Bengtsson, Elizabeth Purdom

References

Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.