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

Description Fields and Methods Author(s) Examples

Package: aroma
Class ExperimentalSetup

Object
~~|
~~+--ExperimentalSetup

Directly known subclasses:

public static class ExperimentalSetup
extends Object

Represents the experimental setup of cDNA microarray experiments. An ExperimentalSetup object contains information about such things as samples used, dyes used for each sample on each hybridization, printing information, scanning information, which the image and data files are etc.

Methods:

	`as.character`	-
	`as.data.frame`	-
	`findSetupFiles`	Locates cDNA microarray experiment setup files.
	`getDataFiles`	-
	`getDyesUsed`	-
	`getImageSoftwaresUsed`	-
	`getLayoutFiles`	-
	`getSampleUsed`	-
	`getScannersUsed`	-
	`nbrOfHybridizations`	-
	`print`	-
	`read`	Reads a file specifying the setup of a microarray experiment.

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

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

  ## Not run: 
  # Due to a bug in R CMD check (R v1.7.1) the MicroarrayData$read() call
  # below will call getKnownSubclasses(), which will generate
  #   "Error in exists(objectName, mode = "function") :
  #	   [2003-07-07 23:32:41] Exception: F used instead of FALSE"
  # Note that the example still work, just not in R CMD check

  setup <- ExperimentalSetup$read("ScanAlyze.setup", path=system.file("misc", package="aroma"))
  print(setup)
  data <- MicroarrayData$read(getDataFiles(setup), path=system.file("misc", package="aroma"))
  raw <- getRawData(data)
  ma <- getSignal(raw)
  subplots(2*nbrOfSlides(ma))
  for (k in seq(ma)) {
    plot(ma, slide=k)
    plotSpatial(ma, slide=k)
  }
  
## End(Not run)