Package: aroma.affymetrix
Class MbeiPlm
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
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~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
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~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MbeiPlm
Directly known subclasses:
MbeiCnPlm, MbeiSnpPlm
public abstract static class MbeiPlm
extends ProbeLevelModel
This class represents the model-based expression indexes (MBEI) multiplicative model in Li & Wong (2001).
MbeiPlm(...)
Arguments passed to ProbeLevelModel.
Methods:
No methods defined.
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
For a single unit group, the multiplicative model is:
$$y_{ik} = \theta_i \phi_k + \varepsilon_{ik}$$
where \(\theta_i\) are the chip effects for arrays \(i=1,...,I\), and \(\phi_k\) are the probe affinities for probes \(k=1,...,K\). The \(\varepsilon_{ik}\) are zero-mean noise with equal variance. To make to parameters identifiable, the constraint \(\prod_k \phi_k = 1\) is added.
Henrik Bengtsson
Li, C. and Wong, W.H. (2001), Genome Biology 2, 1-11.
Li, C. and Wong, W.H. (2001), Proc. Natl. Acad. Sci USA 98, 31-36.
Internally fit.li.wong is used.