AbstractProbeSequenceNormalization {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class AbstractProbeSequenceNormalization
Object
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AromaTransform
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Transform
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ProbeLevelTransform
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ProbeLevelTransform3
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AbstractProbeSequenceNormalization
Directly known subclasses:
BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization
public abstract static class AbstractProbeSequenceNormalization
extends ProbeLevelTransform3
This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in probe sequences.
AbstractProbeSequenceNormalization(..., target=NULL)
... |
Arguments passed to the constructor of
ProbeLevelTransform3 . |
target |
A character string specifying type of "target" used.
If "zero" , all arrays are normalized to have no effects.
If NULL , all arrays a normalized to have the same effect as
the average array has. |
Methods:
getTargetFile | - | |
process | Normalizes the data set. |
Methods inherited from ProbeLevelTransform3:
clearCache, getCellsTo, getCellsToFit, getCellsToUpdate, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
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
This class requires that an AromaCellSequenceFile
is
available for the chip type.
Henrik Bengtsson (http://www.braju.com/R/)