ExonRmaPlm {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ExonRmaPlm
Object
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Model
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UnitModel
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MultiArrayUnitModel
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ProbeLevelModel
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RmaPlm
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ExonRmaPlm
Directly known subclasses:
public 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)
... |
Arguments passed to RmaPlm . |
mergeGroups |
A logical flag specifying whether to merge exons
into transcripts. |
Methods:
calculateWeights | - | |
getCellIndices | - | |
getChipEffects | - | |
getChipEffectSet | - | |
getProbeAffinities | - | |
getProbeAffinityFile | - | |
setMergeGroups | - |
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction
Methods inherited from Model:
fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Ken Simpson (ksimpson[at]wehi.edu.au).
Irizarry et al. Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.