ProbeLevelModel {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ProbeLevelModel
Object
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Model
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UnitModel
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MultiArrayUnitModel
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ProbeLevelModel
Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, RmaCnPlm, RmaPlm, RmaSnpPlm
public 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.
ProbeLevelModel(..., standardize=TRUE)
... |
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. |
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:
RmaPlm
have to transform the parameters on the log-scale to the intensity
scale.
Note that the above probe-affinity constraint guarantees that the estimated chip effects across models are on the same scale.
Methods:
calculateResidualSet | - | |
calculateWeights | - | |
fit | Estimates the model parameters. | |
getChipEffectSet | Gets the set of chip effects for this model. | |
getProbeAffinityFile | Gets the probe affinities for this model. | |
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
Henrik Bengtsson (http://www.braju.com/R/)
For more details on probe-level models, please see the affyPLM package.