AffyRNADegradation: Compute degradation parameters and correct probe intensities

Description Usage Arguments Value Author(s) See Also Examples

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])
}


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