Package: aroma.affymetrix
Class MatNormalization
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--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].
MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)
Arguments passed to the constructor of
AbstractProbeSequenceNormalization.
The units from which the normalization curve should
be estimated. If NULL, all are considered.
A character string specifying the model used to fit
the base-count effects.
The number of bins to use for the variance smoothing step.
Methods:
process | - |
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
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
This class requires that an aroma probe sequence file and aroma match scores file is available for the chip type.
Mark Robinson
[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.