Class AffyDegradationBatch

Description

This class represents Affymetrix GeneChip probe level data that has been analysed and corrected for the probe location bias.

Objects from the Class

Objects can be created using the function RNADegradation.

Slots

location.type:

Object of class character describing the type of probe position used for the analysis (probe index or probe location).

afbatch:

Object of class AffyBatch containing corrected probe level data.

stats:

Object of class matrix containg various statistical parameters from the analysis.

means.pm:

Object of class matrix containing the average PM probe intensites for probe locations of expressed genes.

means.mm:

Object of class matrix containing the average MM probe intensites for probe locations of expressed genes.

Methods

afbatch

signature(x = "AffyDegradationBatch"): returns as AffyBatch object containing corrected probe level data.

d

signature(x = "AffyDegradationBatch"): returns a vector with a measure of RNA degradation for each sample

plotDx

signature(x = "AffyDegradationBatch"): plots the probe location bias for all samples of the experiment.

Author(s)

Mario Fasold

See Also

AffyBatch

Examples

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

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

  ## Plot degradation 
  plotDx(affy.deg)

  ## Get degradation measure
  d(affy.deg)

  ## Get AffyBatch object with corrected probe intensities
  afbatch(affy.deg)
}