BaseCountNormalization: The BaseCountNormalization class

Description

Package: aroma.affymetrix Class BaseCountNormalization Object ~~| ~~+--AromaTransform ~~~~~~~| ~~~~~~~+--Transform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3 ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--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.

Usage

BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)

Arguments

...

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.

Fields and Methods

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, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Requirements

This class requires that an aroma probe sequence file is available for the chip type.