aroma.affymetrix (version 2.2.0)

BasePositionNormalization: The BasePositionNormalization class

Description

Package: aroma.affymetrix Class BasePositionNormalization Object ~~| ~~+--AromaTransform ~~~~~~~| ~~~~~~~+--Transform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3 ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--LinearModelProbeSequenceNormalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--BasePositionNormalization Directly known subclasses: public static class BasePositionNormalization extends LinearModelProbeSequenceNormalization This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in positioning of A, C, G, and T:s in the probe sequences.

Usage

BasePositionNormalization(..., model=c("smooth.spline"), df=5)

Arguments

...

Arguments passed to the constructor of LinearModelProbeSequenceNormalization.

model

A character string specifying the model used to fit the base-count effects.

df

The degrees of freedom of the model.

Fields and Methods

Methods: No methods defined. Methods inherited from LinearModelProbeSequenceNormalization: fitOne, getDesignMatrix, getNormalEquations, getSignalTransform, predictOne 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