ReseqCrosstalkCalibration: The ReseqCrosstalkCalibration class

Description

Package: aroma.affymetrix Class ReseqCrosstalkCalibration Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--ReseqCrosstalkCalibration Directly known subclasses: public static class ReseqCrosstalkCalibration extends ProbeLevelTransform This class represents a calibration function that transforms the probe-level signals such that the signals from the four nucleotides (A, C, G, T) are orthogonal.

Usage

ReseqCrosstalkCalibration(dataSet=NULL, ..., targetAvg=2200, subsetToAvg=NULL,
  mergeGroups=FALSE, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03,
  0.01), q=2, Q=98)

Arguments

dataSet

An AffymetrixCelSet.

...

Arguments passed to the constructor of ProbeLevelTransform.

targetAvg

The signal(s) that the average of the sum of the probe quartets should have after calibration.

subsetToAvg

The indices of the cells (taken as the intersect of existing indices) used to calculate average in order to rescale to the target average. If NULL, all probes are considered.

mergeGroups

A logical ...

flavor

A character string specifying what algorithm is used to fit the crosstalk calibration.

alpha, q, Q

Additional arguments passed to fitMultiDimensionalCone().

Fields and Methods

Methods: rll{ process Calibrates the data set. }

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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis