| MbeiPlm {aroma.affymetrix} | R Documentation |
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 |
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.