BaseCountNormalization {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class BaseCountNormalization
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
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BaseCountNormalization
Directly known subclasses:
public static class BaseCountNormalization
extends AbstractProbeSequenceNormalization
This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s in the probe sequences.
BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)
... |
Arguments passed to the constructor of
AbstractProbeSequenceNormalization . |
model |
A character string specifying the model used to fit
the base-count effects. |
bootstrap |
If TRUE , the model fitting is done by bootstrap in
order to save memory. |
Methods:
No methods defined.
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getTargetFile, indexOfMissingSequences, predictOne, process
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 aroma probe sequence file is available for the chip type.
Henrik Bengtsson (http://www.braju.com/R/)