ProbeLevelModel {aroma.affymetrix}

The ProbeLevelModel class

Description

Package: aroma.affymetrix
Class ProbeLevelModel

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

Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, RmaCnPlm, RmaPlm, RmaSnpPlm

public abstract static class ProbeLevelModel
extends MultiArrayUnitModel

This abstract class represents a probe-level model (PLM) as defined by the affyPLM package: "A [...] PLM is a model that is fit to probe-intensity data. More specifically, it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis", where the more general case for a probeset is a unit group in Affymetrix CDF terms.

Usage

ProbeLevelModel(..., standardize=TRUE)

Arguments

...

Arguments passed to MultiArrayUnitModel.

standardize

If TRUE, chip-effect and probe-affinity estimates are rescaled such that the product of the probe affinities is one.

Details

In order to minimize the risk for mistakes, but also to be able compare results from different PLMs, all PLM subclasses must meet the following criteria:

1. All parameter estimates must be (stored and returned) on the intensity scale, e.g. log-additive models such as RmaPlm have to transform the parameters on the log-scale to the intensity scale.

2. The probe-affinity estimates \phi_k for a unit group must be constrained such that \prod_k \phi_k = 1, or equivalently if \phi_k > 0,\sum_k \log(\phi_k) = 0.

Note that the above probe-affinity constraint guarantees that the estimated chip effects across models are on the same scale.

Fields and Methods

Methods:

	fit	-
	getChipEffectSet	-
	getProbeAffinityFile	-
	getResidualSet	-
	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

Author(s)

Henrik Bengtsson

See Also

For more details on probe-level models, please see the preprocessCore package.