AffyRNAdeg: Function to assess RNA degradation in Affymetrix GeneChip...

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

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)
}

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.