AffyRNADegradation: Compute degradation parameters and correct probe intensities

In AffyRNADegradation: Analyze and correct probe positional bias in microarray data due to RNA degradation

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

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

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

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

AffyRNADegradation documentation built on Nov. 8, 2020, 5:36 p.m.