MbeiPlm: The MbeiPlm class

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

The MbeiPlm class

Description

Package: aroma.affymetrix
Class MbeiPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--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).

Usage

MbeiPlm(...)

Arguments

...	Arguments passed to ProbeLevelModel.

Fields and Methods

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

Model

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.

Author(s)

Henrik Bengtsson

References

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.

See Also

Internally fit.li.wong is used.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.