affy (version 1.50.0)

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.

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

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.

Examples

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