MatNormalization: The MatNormalization class
Description
Package: aroma.affymetrix
Class MatNormalization
Object
~~|
~~+--AromaTransform
~~~~~~~|
~~~~~~~+--Transform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MatNormalization
Directly known subclasses:
public static class MatNormalization
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 and the match scores according to MAT [1].Usage
MatNormalization(..., unitsToFit=NULL, model=c("lm"), numChunks=25, numBins=200)Arguments
unitsToFit
The units from which the normalization curve should
be estimated. If NULL, all are considered. model
A character string specifying the model used to fit
the base-count effects. numChunks
The number of chunks to split the data into to
fit the model
numBins
The number of bins to use for the variance smoothing step
Fields and Methods
Methods:
rll{
process Normalizes the data set.
}
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, saveRequirements
This class requires that an aroma probe sequence file and aroma
match scores file is available for the chip type.References
[1] Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS.
Model-based analysis of tiling-arrays for ChIP-chip, PNAS, 2006.