Compute degradation parameters and correct probe intensities

Description

Given an AffyBatch object, the function RNADegradation computes the probe positional bias and several statistical parameters, including a robust and accurate measure of RNA degradation. Probe intensities are corrected for the bias for each sample within the AffyBatch object.

Usage

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RNADegradation(affyData,
               location.type = "index",
               location.file.dir = NULL,
               plot.images = FALSE)

Arguments

affyData

an AffyBatch object containing the probe level microarray data.

location.type

index-based probe alignment (x=k) if "index", or location-based alignment (x=L) if "absolute".

location.file.dir

directory containing the probe location file(s).

plot.images

if TRUE plots a set of debug images.

Value

An AffyDegradationBatch object.

Author(s)

Mario Fasold

See Also

AffyDegradationBatch

Examples

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

  affy.deg <- RNADegradation(AmpData[,4])
}