AffyRNADegradation: analyze and correct RNA degradation effects

Description

The AffyRNADegradation package helps in the assessment of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Details

Package: AffyRNADegradation
Type: Package
Version: 0.1.0
Date: 2011-10-13
License: GPL >=2

The RNADegradation function performs both analysis and correction of RNA degradation effects, returning an object of type AffyDegradationBatch. The class provides accessor functions to obtain the degradation parameter d and a AffyBatch object containing corrected probe intensities. A more detailed look on the RNA degradation effects can be gained through the tongs plot, the Dx plot and further statistics.

Author(s)

Mario Fasold

Examples

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if (require(AmpAffyExample)) {
  # Load example data (AmpData affybatch)
  data(AmpData)

  ## Compute and correct degradation for a single chip (for speed)
  affy.deg <- RNADegradation(AmpData[,4])

  ## Show degradation parameter d  
  d(affy.deg)

  ## Replace data with corrected data for further analysis
  AmpData <- afbatch(affy.deg)
}