ScaleNormalization {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ScaleNormalization
Object
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AromaTransform
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Transform
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ProbeLevelTransform
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ScaleNormalization
Directly known subclasses:
public static class ScaleNormalization
extends ProbeLevelTransform
This class represents a normalization function that transforms the probe-level signals towards the same scale.
ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL, typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)
dataSet |
AffymetrixCelSet to be normalized. |
... |
Arguments passed to the constructor of
ProbeLevelTransform . |
targetAvg |
A numeric value. |
subsetToUpdate |
The probes to be updated.
If NULL , all probes are updated. |
typesToUpdate |
Types of probes to be updated. |
subsetToAvg |
The probes to calculate average signal over.
If a single numeric in (0,1), then this
fraction of all probes will be used.
If NULL , all probes are considered. |
typesToAvg |
Types of probes to be used when calculating the
average signal.
If "pm" and "mm" only perfect-match and mismatch
probes are used, respectively. If "pmmm" both types are used.
|
shift |
Optional amount of shift if data before fitting/normalizing. |
Methods:
process | Normalizes the data set. |
Methods inherited from Transform:
getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles
Methods inherited from AromaTransform:
getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, 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/)