swapDyes.MAData: Dye swap one or many slides
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Value Author(s) See Also Examples

Dye swap one or many slides.

1 2	## S3 method for class 'MAData' swapDyes(this, slides=NULL, ...)

slides

A vector of slides to be dye swapped. If NULL, all slides are considered.

Returns itself.

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

For more information see MAData.

  # The option 'dataset' is used to annotate plots.
  options(dataset="sma:MouseArray")

  SMA$loadData("mouse.data")
  layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
  raw <- RawData(mouse.data, layout=layout)

  ma <- getSignal(raw, bgSubtract=TRUE)
  rg <- as.RGData(ma)

  # Dye swap every other slide.
  swapDyes(ma, slides=c(4,5,6))

  layout(matrix(1:6, nrow=2, ncol=3, byrow=TRUE));
  for (k in 1:6)
    plot(ma, slide=k)