getRawData.SpotData: Gets the raw intensites from the SpotData structure

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

Description

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

Usage

## S3 method for class 'SpotData'
getRawData(this, slides=NULL, fgs="auto", bgs="auto", ...)

Arguments

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. To get the mean of the median of the background intensites in the four diamond shaped ares around the spots, use the value "valley". There are also three morphological background estimates; morph, morph.erode, and morph.close.open.

Details

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

Value

Returns a RawData object containing the specified slides.

Author(s)

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

See Also

For more information see SpotData.

Examples

## Not run: # For an example see help(SpotData).

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.