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).ExonRmaPlm(..., mergeGroups=TRUE)RmaPlm.logical flag specifying whether to merge exons
into transcripts.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, getParameterSet, 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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis
RmaPlm.