QuantileNormalization | R Documentation |
Package: aroma.affymetrix
Class QuantileNormalization
Object
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ParametersInterface
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AromaTransform
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Transform
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ProbeLevelTransform
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QuantileNormalization
Directly known subclasses:
DChipQuantileNormalization
public static class QuantileNormalization
extends ProbeLevelTransform
This class represents a normalization function that transforms the probe-level signals towards the same empirical distribution.
QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL, targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)
... |
Arguments passed to the constructor of
|
subsetToUpdate |
The probes to be updated.
If |
typesToUpdate |
Types of probes to be updated. |
targetDistribution |
A |
subsetToAvg |
The probes to calculate average empirical
distribution over. If a single |
typesToAvg |
Types of probes to be used when calculating the
average empirical distribution.
If |
Methods:
process | - | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
## Not run: for (zzz in 0) { # Setup verbose output verbose <- Arguments$getVerbose(-2) timestampOn(verbose) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define an example dataset # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Find any dataset path <- NULL if (is.null(path)) break ds <- AffymetrixCelSet$fromFiles(path) print(ds) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Normalization # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - norm <- QuantileNormalization(ds, subsetToAvg=1/3) dsQN <- process(norm, verbose=verbose) print(dsQN) } # for (zzz in 0) rm(zzz) ## End(Not run)
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