getRawData.ScanAlyzeData: Gets the raw (foreground and background) intensites
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Details Value Author(s) See Also Examples

Extracts the red and green spot intensitites (both foreground and background) and returns a RawData object.

1 2	## S3 method for class 'ScanAlyzeData' getRawData(this, slides=NULL, fg=c("auto"), bg=("auto"), ...)

`slides`	Specifying which slides to be extracted. If `NULL`, all slides are considered.
`fg`	If `"auto"`, the default foreground estimates according to `*getForeground()` is returned.
`bg`	If `"auto"`, the default foreground estimates according to `*getBackground()` is returned.

The R and Rb channels will come from the CH2* fields, and the G and Gb channels will come from the CH1* fields. To swap the channels just use dyeSwap().

Returns a RawData object containing the specified slides.

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

For more information see ScanAlyzeData.

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

  # Get the foreground and the background
  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)