ReseqCrosstalkCalibration: The ReseqCrosstalkCalibration class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

ReseqCrosstalkCalibration

R Documentation

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:

	`process`	-

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