ScanAlyzeData: The ScanAlyzeData class

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

Description

Package: aroma
Class ScanAlyzeData

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--ScanAlyzeData

Directly known subclasses:
ScanAlyze20Data

public static class ScanAlyzeData
extends MicroarrayData

Creates an empty ScanAlyzeData object.

Usage

ScanAlyzeData(layout=NULL)

Arguments

layout

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

Fields and Methods

Methods:

	append	-
	as.RawData	-
	getArea	-
	getBackground	-
	getBgArea	-
	getCircularity	-
	getDiameter	-
	getForeground	-
	getGrid	-
	getRawData	Gets the raw (foreground and background) intensites.
	getSpotColumn	-
	getSpotPosition	Gets physical positions of the spots.
	getSpotRow	-
	normalizeGenewise	-
	plotSpatial	Creates a spatial plot of a slide.
	plotSpatial3d	-
	read	Reads one or several ScanAlyze files into a ScanAlyzeData object.
	write	Write a ScanAlyze 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

Details

A ScanAlyze file contains spot information for each spot on a single microarray slide. It consists of a header followed by a unspecified number of rows. The header contains a number of field labels. Each row starting with SPOT corresponds to one spot. Other rows starts with HEADER or REMARK. The spot fields are:

\item

SPOTUnique index of spot in file. "Counting starts with grid 1, moves along row 1 from column 1 until the last column, then advances to the next row; after all rows in grid 1 are assigned an index, counting proceeds to grid 2, etc.". Comment: This is the same way as GenePix and Spot indices the spots. \itemGRIDGrid number. \itemTOP, LEFT, BOT, RIGHTCoordinates of the box containing spot ellipse, in image coordinates. \itemROWRow within grid. \itemCOLColumn within grid. \itemCH1I, CH2IChannel 1,2 - uncorrected mean of the foreground pixel intensites. \itemCH1B, CH2BChannel 1,2 - median of the background pixel intensites. \itemCH1BA, CH2BAChannel 1,2 - mean of the background pixel intensites. \itemSPIXNumber of pixels in the foreground, i.e. in the spot. \itemBGPIXNumber of pixels in the background. \itemEDGE? \itemRAT2Median of (CH2PI-CH2B)/(CH1PI-CH1B) where CH1PI and CH2PI are the single pixel intensities. \itemMRAT? \itemREGR? \itemCORRThe correlation between channel1 and channel2 pixels within the spot. \itemLFRAT? \itemCH1GTB1, CH2GTB1Fraction of pixels in the spot greater than the background (CH1B or CH2B). \itemCH1GTB2, CH2GTB2Fraction of pixels in the spot greater than 1.5 times the background (CH1B or CH2B). \itemCH1EDGEA, CH2EDGEAmean magnitude of the horizontal and vertical Sobel edge vectors within spot 1 and spot 2, respectively \itemFLAGUser defined spot flag (default 0). \itemCH1KSD, CH2KSDThe value of the Komogorov-Smirnov statistic [3] that assesses the likelihood that the spot pixel intensity distribution is drawn from the background distribution. \itemCH1KSP, CH2KSPThe actual probabilities of the above statistic.

Note

The laser beam with wavelength 635nm is the red laser, and the one with wavelength 532nm is the green laser.

Author(s)

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

References

[1] ScanAlyze Software, Eisen Lab, Lawrence Berkeley National Lab, 2001, http://rana.lbl.gov/EisenSoftware.htm.
[2] ScanAlyze User Manual, Michael Eisen, Stanford University, 1999, http://rana.lbl.gov/manuals/ScanAlyzeDoc.pdf.
[3] 14.3 Are Two Distributions Different? a sample chapter from Numerical Recipes in C: The Art of Scientific Computing, 1992, Cambridge University Press http://www.ulib.org/webRoot/Books/Numerical_Recipes/bookcpdf/c14-3.pdf.

Examples

  sa <- ScanAlyzeData$read("group4.dat", path=system.file("data-ex", package="aroma"))

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

  # 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.