getForegroundSD.GenePixData: Gets the standard deviation of the foreground pixels

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

Description

Gets the standard deviation of the foreground pixels.

Usage

## S3 method for class 'GenePixData'
getForegroundSD(this, slides=NULL, channels=1:2, ...)

Details

The GenePix fields "F532 SD" (green) and "F635 SD" (red) are returned.

Value

Returns a list of matrices that contain the estimated standard deviation of the pixels in the foreground region of the spots.

Author(s)

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

See Also

For more information see GenePixData.

Examples

  gpr <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))
  raw <- getRawData(gpr)
  sd <- getForegroundSD(gpr)
  raw$RSD <- sd$RSD; raw$GSD <- sd$GSD;
  sd <- getBackgroundSD(gpr)
  raw$RbSD <- sd$RbSD; raw$GbSD <- sd$GbSD;
  subplots(4)
  plot(raw, "RSDvsR", col="red")
  plot(raw, "RbSDvsRb", col="red")
  plot(raw, "GSDvsG", col="green")
  plot(raw, "GbSDvsGb", col="green")

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