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, objectSize, print, save, asThis

Model

RmaPlm.

References

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