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

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

Package: aroma
Class ImaGeneData

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--ImaGeneData

Directly known subclasses:

public static class ImaGeneData
extends MicroarrayData

Creates an empty ImaGeneData object.

1	ImaGeneData(layout=NULL)

layout

A Layout object specifying the spot layout of the slides in this data set.

Methods:

	`anonymize`	-
	`as.RawData`	-
	`getAbscent`	-
	`getArea`	-
	`getBgArea`	-
	`getCircularity`	-
	`getRawData`	Gets the raw intensites from two ImaGeneData objects.
	`getSpotPosition`	Gets physical positions of the spots.
	`plotSpatial`	-
	`plotSpatial3d`	-
	`read`	Reads an ImaGene result file.
	`setLayout`	-
	`write`	Write an ImaGene result data file.

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

The laser beam with wavelength 635nm is the red laser and excites the Cy5 dye, and the one with wavelength 532nm is the green laser which excites the Cy3 dye.

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

BioDiscovery's ImaGene software, http://www.biodiscovery.com/imagene.asp

######################################################################
# Example that reads two ImaGene data files, which are single-channel
# and represent one slide, and combines them into a RawData object.
######################################################################
igG <- ImaGeneData$read("imagene234.cy3", path=system.file("data-ex", package="aroma"))
igR <- ImaGeneData$read("imagene234.cy5", path=system.file("data-ex", package="aroma"))

# Get the raw data; Rfg, Gfg, Rbg and Gbg
raw <- getRawData(igR, igG)

# The the background corrected data
ma <- getSignal(raw)

# Plot M vs A with a lowess line through the data points
subplots(4)
plot(ma)
plotSpatial(ma)
boxplot(ma, groupBy="printtip")


######################################################################
# Example that reads multiple ImaGene data files, which all are
# single-channel and represent several slide, and then combines them
# into a RawData object of several slides.
######################################################################

# Function that reads several (single-channel) ImaGene data files
# and combines them into a multi-slide two-channel RawData object
myImaGeneReadAll <- function(slides, extensions=c("cy3","cy5"), ...) {
  # An empty RawData object to store all slides
  raw <- RawData()
  for (slide in slides) {
    igCy3 <- ImaGeneData$read(paste(slide, extensions[1], sep="."), ...)
    igCy5 <- ImaGeneData$read(paste(slide, extensions[2], sep="."), ...)
    tmp <- getRawData(igCy3, igCy5)
    append(raw, tmp)
  }

  # Return the RawData object containing all slides
  raw;
} # myImaGeneReadAll()


# "Faking" three slides...
slides <- rep("imagene234", 3)

# ...and reads them.
raw <- myImaGeneReadAll(slides, path=system.file("data-ex", package="aroma"))