Package 'AffyRNADegradation'

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)
}

---

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

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)
}

---

Generate and visualize the tongs plot

Description

The tongs plot and the related degradation hook show the relationship between expression level and probe location bias. They are required for the correct estimation of RNA degradation effects.

Usage

GetTongs(affyData, chip.idx = 1)
PlotTongs(tongs)
PlotDegradationHooks(affyData, ...)

Arguments

affyData	an AffyBatch object.
chip.idx	index of the sample to compute the tongs for.
tongs	the tongs plot data table.
...	optional graphical parameters.

Value

Tongs

a table containing Tongs plot values ordered by expression level.

Author(s)

Mario Fasold

Examples

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

  tongs <- GetTongs(AmpData, chip.idx = 4)
  PlotTongs(tongs)

  PlotDegradationHooks(AmpData[,c(3,4)])
}

---

Compute degradation parameters and correct probe intensities

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])
}

---