AvgPlm {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class AvgPlm
Object
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~~+--
Model
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UnitModel
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MultiArrayUnitModel
~~~~~~~~~~~~~~~~~|
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ProbeLevelModel
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AvgPlm
Directly known subclasses:
AvgCnPlm, AvgSnpPlm
public static class AvgPlm
extends ProbeLevelModel
This class represents a PLM where the probe intensities are averaged assuming identical probe affinities. For instance, one may assume that replicated probes with identical sequences have the same probe affinities, cf. the GenomeWideSNP_6 chip type.
AvgPlm(..., flavor=c("median", "mean"))
... |
Arguments passed to ProbeLevelModel . |
flavor |
A character string specifying what model fitting algorithm
to be used. This makes it possible to get identical estimates as other
packages. |
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
For a single unit group, the averaging PLM of K probes is:
y_{ik} = theta_i + varepsilon_{ik}
where theta_i are the chip effects for arrays i=1,...,I. The varepsilon_{ik} are zero-mean noise with equal variance.
The above model can be fitted in two ways, either robustly or
non-robustly.
Use argument flavor="mean"
to fit the model non-robustly, i.e.
hat{theta}_{i} = 1/K sum_k y_{ik}
.
Use argument flavor="median"
to fit the model robustly, i.e.
hat{theta}_{i} = median_k y_{ik}
.
Missing values are always excluded.
Henrik Bengtsson (http://www.braju.com/R/)