MbeiPlm: 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, 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

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.

References