MbeiPlm {aroma.affymetrix}R Documentation

The MbeiPlm class

Description

Package: aroma.affymetrix
Class MbeiPlm

Object
~~|
~~+--Model
~~~~~~~|
~~~~~~~+--UnitModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--MbeiPlm

Directly known subclasses:
MbeiCnPlm, MbeiSnpPlm

public static class MbeiPlm
extends ProbeLevelModel

This class represents the multiplicative model in Li & Wong (2001).

Usage

MbeiPlm(...)

Arguments

... Arguments passed to ProbeLevelModel.

Fields and Methods

Methods:
getAsteriskTags -

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

Model

For a single unit group, the multiplicative model of dChip 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 (http://www.braju.com/R/)

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.


[Package aroma.affymetrix version 1.2.0 Index]