AffyRNAdeg {affy}R Documentation

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 tranformed
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

data(affybatch.example)
RNAdeg<-AffyRNAdeg(affybatch.example)
plotAffyRNAdeg(RNAdeg)


[Package affy version 1.8.1 Index]