AffyRNADegradation-package: AffyRNADegradation: analyze and correct RNA degradation...

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

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

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)
}

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