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.
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)
An AffymetrixCelSet.
Arguments passed to the constructor of
ProbeLevelTransform.
The signal(s) that the average of the sum of the probe quartets should have after calibration.
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.
A logical ...
A character string specifying what algorithm is used
to fit the crosstalk calibration.
Additional arguments passed to
fitMultiDimensionalCone().
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
Henrik Bengtsson