RawData: The RawData class
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Fields and Methods Note Author(s) Examples

Package: aroma
Class RawData

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--RawData

Directly known subclasses:

public static class RawData
extends MicroarrayData

Creates a new RawData object.

1	RawData(R=NULL, G=NULL, Rb=NULL, Gb=NULL, layout=NULL, extras=list())

`R,G`	A NxM `matrix` containing (non-logged) foreground signals of the red (green) channel, where N is the number of spots on each slide and M is the number of slides in this data set.
`Rb,Gb`	A NxM `matrix` containing (non-logged) background signals of the red (green) channel, where N is the number of spots on each slide and M is the number of slides in this data set.
`layout`	A `Layout` object specifying the spot layout of the slides in this data set.
`extras`	Private argument. Do not use.

	`R`	The foreground for channel R (non-logged).
	`G`	The foreground for channel G (non-logged).
	`Rb`	The background for channel Rb (non-logged).
	`Gb`	The background for channel Gb (non-logged).

Methods:

	`as.character`	-
	`as`	-
	`as.RawData`	-
	`as.RGData`	-
	`boxplot`	-
	`calibrateMultiscan`	-
	`getBackground`	Gets the background signal.
	`getColors`	Generates colors for each of the specified spots.
	`getForeground`	Gets the foreground signal.
	`getSignal`	Gets the red and the green signal.
	`getSNR1`	-
	`getSNR2`	-
	`getWithinChannelPairs`	-
	`normalizeAffine`	-
	`normalizeGenewise`	-
	`normalizeQuantile`	-
	`normalizeWithinSlide`	-
	`plot`	-
	`plotSpatial`	-
	`plotXY`	-
	`range`	-
	`shift`	Shift the log-ratios, log-intensities or the raw signal.
	`swapDyes`	Dye swap one or many slides.

Methods inherited from MicroarrayData:
addFlag, append, applyGenewise, applyGroupwise, applyPlatewise, applyPrintdipwise, applyPrinttipwise, as.character, as.data.frame, boxplot, clearCache, clearFlag, createColors, dataFrameToList, equals, extract, getBlank, getCache, getChannelNames, getColors, getExcludedSpots, getExtra, getExtreme, getFieldNames, getFlag, getInclude, getLabel, getLayout, getProbeWeights, getSignalWeights, getSlideNames, getSlidePairs, getSpotPosition, getSpotValue, getTreatments, getView, getWeights, getWeightsAsString, hasExcludedSpots, hasLayout, hasProbeWeights, hasSignalWeights, hasWeights, highlight, hist, isFieldColorable, keepSlides, keepSpots, listFlags, lowessCurve, nbrOfDataPoints, nbrOfFields, nbrOfSlides, nbrOfSpots, nbrOfTreatments, normalizePlatewise, normalizePrintorder, normalizeQuantile, plot, plotDensity, plotGene, plotPrintorder, plotReplicates, plotSpatial, plotSpatial3d, plotXY, points, putGene, putSlide, qqnorm, quantile, range, range2, read, readHeader, readToList, removeSlides, removeSpots, resetProbeWeights, resetSignalWeights, select, seq, setCache, setExcludedSpots, setExtra, setFlag, setLabel, setLayout, setProbeWeights, setSignalWeights, setSlideNames, setTreatments, setView, setWeights, size, str, subplots, summary, text, updateHeader, validateArgumentChannel, validateArgumentChannels, validateArgumentGroupBy, validateArgumentSlide, validateArgumentSlides, validateArgumentSpotIndex, validateArgumentWeights, write, writeHeader

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

There are several functions that returns an object of this class, and it is only in very special cases that you actually have to create one yourself.

Henrik Bengtsson (http://www.braju.com/R/)