Generate and visualize the tongs plot

Description

The tongs plot and the related degradation hook show the relationship between expression level and probe location bias. They are required for the correct estimation of RNA degradation effects.

Usage

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GetTongs(affyData, chip.idx = 1)
PlotTongs(tongs)
PlotDegradationHooks(affyData, ...)

Arguments

affyData

an AffyBatch object.

chip.idx

index of the sample to compute the tongs for.

tongs

the tongs plot data table.

...

optional graphical parameters.

Value

Tongs

a table containing Tongs plot values ordered by expression level.

Author(s)

Mario Fasold

Examples

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if (require(AmpAffyExample)) {
  # Get example data
  data(AmpData)

  tongs <- GetTongs(AmpData, chip.idx = 4)
  PlotTongs(tongs)

  PlotDegradationHooks(AmpData[,c(3,4)])
}