getRawData.GenePixData: Gets the raw intensites from the GPR structure
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

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

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

Note: From com.braju.sma v0.59, this method returns the *median* foreground and background estimates. Previous versions returned the *mean* of dito.

1 2	## S3 method for class 'GenePixData' getRawData(this, slides=NULL, fg="median", bg="median", channels=1:2, ...)

`slides`	Specifying which slides to be extracted. If `NULL`, all slides are considered.
`fg`	If `"mean"`, the mean foreground intensities are returned. If `"median"`, the median foreground intensities are returned.
`bg`	If `"mean"`, the mean background intensities are returned. If `"median"`, the median background intensities are returned.
`channels`	A `vector` of length two specifying which two channels (wavelengths) to be extracted in case the data contains more than two channels (colours).

The R and Rb channels will come from the F635* and B635* fields, and the G and Gb channels will come from the F532* and B532* fields. To swap the channels just use dyeSwap().

From com.braju.sma v0.30 the dye.swap argument has been removed. Any dye swapping should be done bye using the dyeSwap() method.

Returns a RawData object containing the specified slides.

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

GenePix File Formats, http://www.axon.com/GN_GenePix_File_Formats.html

For more information see GenePixData.

  gpr <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))

  # Gets the foreground and the background
  raw <- getRawData(gpr)