ReseqCrosstalkCalibration {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ReseqCrosstalkCalibration
Object
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AromaTransform
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Transform
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ProbeLevelTransform
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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)
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 |
Methods:
clearCache | - | |
process | Calibrates 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, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Henrik Bengtsson (http://www.braju.com/R/)