GcContentNormalization: The GcContentNormalization class

Description

Package: aroma.affymetrix Class GcContentNormalization Object ~~| ~~+--AromaTransform ~~~~~~~| ~~~~~~~+--Transform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--ChipEffectTransform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--GcContentNormalization Directly known subclasses: public static class GcContentNormalization extends ChipEffectTransform

Usage

GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)

Arguments

dataSet

A CnChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

targetFunction

A function. The target function to which all arrays should be normalized to.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

Fields and Methods

Methods: rll{ getCdf - getOutputDataSet00 - process Normalizes the data set. } 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 an Aroma unit GC-content (UGC) file.