Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

AffyRNAdeg

Function to assess RNA degradation in Affymetrix GeneChip data.


Description

Uses ordered probes in probeset to detect possible RNA degradation. Plots and statistics used for evaluation.

Usage

AffyRNAdeg(abatch,log.it=TRUE)
summaryAffyRNAdeg(rna.deg.obj,signif.digits=3)
plotAffyRNAdeg(rna.deg.obj, transform = "shift.scale", cols = NULL, ...)

Arguments

abatch

An object of class AffyBatch-class.

log.it

A logical argument: If log.it=T, then probe data is log2 transformed.

rna.deg.obj

Output from AffyRNAdeg.

signif.digits

Number of significant digits to show.

transform

Possible choices are "shift.scale","shift.only", and "neither". "Shift" vertically staggers the plots for individual chips, to make the display easier to read. "Scale" normalizes so that standard deviation is equal to 1.

cols

A vector of colors for plot, length = number of chips.

...

further arguments for plot function.

Details

Within each probeset, probes are numbered directionally from the 5' end to the 3' end. Probe intensities are averaged by probe number, across all genes. If log.it=FALSE and transform="Neither", then plotAffyRNAdeg simply shows these means for each chip. Shifted and scaled versions of the plot can make it easier to see.

Value

AffyRNAdeg returns a list with the following components:

sample.names

names of samples, derived from affy batch object

means.by.number

average intensity by probe position

ses

standard errors for probe position averages

slope

from linear regression of means.by.number

pvalue

from linear regression of means.by.number

Author(s)

Leslie Cope

Examples

if (require(affydata)) {
  data(Dilution)
  RNAdeg<-AffyRNAdeg(Dilution)
  plotAffyRNAdeg(RNAdeg)
}

affy

Methods for Affymetrix Oligonucleotide Arrays

v1.68.0
LGPL (>= 2.0)
Authors
Rafael A. Irizarry <rafa@ds.harvard.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.