GenePixData: The GenePixData class

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

Description

Package: aroma
Class GenePixData

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--GenePixData

Directly known subclasses:

public static class GenePixData
extends MicroarrayData

Usage

GenePixData(layout=NULL, ...)

Arguments

layout	A Layout object specifying the spot layout of the slides in this data set.
...	Not used.

Details

For information about the fields in this class see Axon's specifications of the GenePix File Formats at http://www.axon.com/GN_GenePix_File_Formats.html.

Fields and Methods

Methods:

	anonymize	-
	append	-
	as.RawData	-
	getAbscent	-
	getArea	Gets the area of the spot.
	getArrayAspectRatio	-
	getArrayBottom	-
	getArrayHeight	-
	getArrayLeft	-
	getArrayRight	-
	getArrayTop	-
	getArrayWidth	-
	getBackground	-
	getBackgroundArea	-
	getBackgroundSD	Gets the standard deviation of the background pixels.
	getBad	-
	getCircularity	-
	getFocusPosition	-
	getForeground	-
	getForegroundSD	Gets the standard deviation of the foreground pixels.
	getForegroundSE	Gets the standard error of the foreground pixels.
	getLaserOnTime	-
	getLaserPower	-
	getLinesAveraged	-
	getNotFound	-
	getPixelSize	-
	getPMTGain	-
	getRawData	Gets the raw intensites from the GPR structure.
	getRgn R2	-
	getSpotPosition	Gets physical positions of the spots.
	getTemperature	-
	getWavelengths	-
	normalizeGenewise	-
	plotSpatial	Creates a spatial plot of a slide.
	plotSpatial3d	-
	read	Reads one or several GenePix files into one GenePixData object.
	readHeader	Reads a GenePix Results (GPR) file header.
	setLayout	-
	write	Write a GenePix Results 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

Flagging feature-indicators

GenePix Pro can flags individual spots according to different criterias. The different flag statuses are Good (has value 100 in the GPR structure), Bad (-100), absent (-75), and Not Found (-50). Unflagged spots have value 0. A spot can only have one of these flags set at each time.

The Absent flag is set automatically if there is a blank/empty entry in the GAL file (commonly reflected in the Layout object associated with this GenePixData object).

The Not Found flag is set automatically if the spot/block alignment failed to find the spot. The position and diameter reported for such a spot are taken from the initial values obtained from the rough gridding. Note that the spot signals are still estimated. It may happen that the spot is dislocated, but that the user can visually pick it up and recenter the spot position and ask GenePix Pro to resegment the spot. The result may then be that GenePix flags the spot as Good or Not Found if it still finds that the spot is too weak for segmentation.

The Bad and Good flags are set manually by the user. A typical scenario is that GenePix identified the spots to have strong signals and segmented them well, but when the user looks at the image she or he sees that two spots are overlapping and have probably mixed their contents. Then the user flags that spot as Bad. It can also be that there is a spot of interest, say a negative control, and GenePix flags it as Not Found, but the users looks at it and concludes that it is indeed a high quality negative control spot and therefore flags it as Good.

Spots that have been flagged Absent, Bad, and Good (not sure about this last one), will not be relabel by GenePix. Thus, GenePix will only flag or unflag spots that are Not Found or unflagged.

Note that any flag may be set or unset manually after the automatic flagging has been done.

Note

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.

Author(s)

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

References

GenePix File Formats, http://www.axon.com/GN_GenePix_File_Formats.html and http://meetings.cshl.org/tgac/tgac/microarray.html

Examples

   gpr <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))

   # Get the foreground and the background (and the layout)
   raw <- getRawData(gpr)

   # The the background corrected data
   ma <- getSignal(raw, bgSubtract=FALSE)

   # Plot M vs A with a lowess line through the data points
   plot(ma, slide=1)
   lowessCurve(ma, lwd=2, gridwise=TRUE)
 

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.