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

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

Package: aroma
Class QuantArrayData

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--QuantArrayData

Directly known subclasses:

public static class QuantArrayData
extends MicroarrayData

Creates an empty QuantArrayData object.

1	QuantArrayData(layout=NULL)

layout

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

\item

ch1 Intensity, ch2 Intensity, ...The spot intensity. What the authors mean by intensity is not clear, but on p46 in [2] it says "Quantitation. Output allows the user to choose the way the spot intensities are calculated: a) the sum of the intensities for the various pixels of the spot and the background (Total Intensities), b) the average of the intensities (Mean Intensity), c) the most frequent occurrence of a pixel value (Mode Intensity), or d) the Median Intensity can be reported."

If this is true, then where is the information about which method was used? Looking at the header of a typical QuantArray data file this information is not stored anywhere. \itemch1 Intensity Std Dev, ch2 Intensity Std Dev, ... The standard deviation of the spot pixel intensities. \itemch1 Spot Uniformity, ch2 Spot Uniformity, ... Value in [0,1]. The 0.99 quantile minus the 0.01 quantile pixel signal divided by the pixel intensity range.

\item

ch1 Background, ch2 Background, ...The background intensity. \itemch1 Background Std Dev, ch2 Background Std Dev, ... The standard deviation of the background pixel intensities. \itemch1 Bkg. Uniformity, ch2 Bkg. Uniformity, ...Value in [0,1].

\item

ch1 Diameter, ch2 Diameter, ...The average spot diameter (in micrometers). \itemch1 Area, ch2 Area, ...The spot area as the number of pixels (in square micrometers). \itemch1 Footprint, ch2 Footprint, ...The distance (in micrometers) between the expected position of the spot and its actual position. \itemch1 Circularity, ch2 Circularity, ... Value in [0,1]. The circularity. \itemch1 Replicate Uniformity, ch2 Replicate Uniformity, ... Value in [0,1]. Uniformity of replicated spots.

\item

ch1 Confident, ch2 Confident, ... Value in [0,1]. Different methods may have been used. See in sections[["Protocol Info"]] of the QuantArrayData object which was used. Let (c[1], c[2], ..., c[Q]) be the individual measurement confidences. Then "Minimum") cAll = min(c). "Weighted Average") cAll = sum(w*c)/sum(w) where w are weights. "Product") cAll = (prod(c))^(1/Q).

Redundant fields:
\itemch1 Percentage, ch2 Percentage, ...REDUNDANT! =="ch1 Intensity"/("ch1 Intensity"+"ch2 Intensity") and so on. For each spot, the percentage of the total brightness (the sum of all channels' intensities) for each channel. \itemch1 Ratio, ch2 Ratio, ...REDUNDANT! =="ch2 Intensity"/"ch1 Intensity" or similar. For each spot, the relative intensity of a spot, compared to the corresponding spot in the control. The ratio value for the channel that is the control channel (commonly channel 1) are all equal to 1. The ratio value for the other channels are equal to their relative ratio of the intensity compared to the control. Background subtraction might have been applied first, but that is still reduandant. \itemch1 Signal Noise Ratio, ch2 Signal Noise Ratio, ... REDUNDANT! =="ch1 Intensity"/"ch1 Background Std Dev" and so on. The ratio of the spot intensity to the standard deviation of the local background of all spots in the microarray.

Sources: Our own "research" and [2].

Methods:

	`anonymize`	-
	`as.RawData`	-
	`getArea`	-
	`getBackground`	-
	`getBackgroundSD`	-
	`getForeground`	-
	`getForegroundSD`	-
	`getForegroundSNR`	-
	`getRawData`	Gets the raw intensites from the QuantArray data structure.
	`getSpotPosition`	Gets physical positions of the spots.
	`plotSpatial`	Creates a spatial plot of a slide.
	`plotSpatial3d`	-
	`read`	Reads one or several QuantArray files into one QuantArrayData object.
	`setLayout`	-
	`write`	Write a QuantArray 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/)

[1] QuantArray software by PerkinElmer Life Sciences, http://lifesciences.perkinelmer.com/.
[2] Packard BioScience, QuantArray Microarray Analysis Software Manual, 2001.

 ## Not run: 
  # At the moment there is no QuantArray sample files in the package...
  # qa <- QuantArrayData$read("quantarray123.txt", path=system.file("data-ex", package="aroma"))
  # ...will use a GenePix sample file instead.
  qa <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))

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

  # 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")
 
## End(Not run)