xps (version 1.32.0)

AffyRNAdeg: Functions to assess RNA Degradation.

Description

Functions to detect possible RNA degradation.

Usage

AffyRNAdeg(xps.data, treename = "*", qualopt = "raw", log.it = TRUE)
summaryAffyRNAdeg(rna.deg, signif.digits=3)
plotAffyRNAdeg(rna.deg, transform = "shift.scale", col = NULL, summary = FALSE, add.legend = FALSE, ...)
xpsRNAdeg(object, ...)

Arguments

xps.data

object of class QualTreeSet.

treename

vector of tree names to export.

qualopt

option determining the data to which to apply qualification, one of ‘raw’, ‘adjusted’, ‘normalized’.

log.it

logical, if TRUE, then probe data is log2 transformed.

rna.deg

list, output from AffyRNAdeg.

signif.digits

number of significant digits to show.

transform

transform data before plotting, one of "shift.scale", "shift.only", "none".

col

vector of colors for plot, length is number of samples.

summary

logical, if TRUE then the slope of summaryAffyRNAdeg will be plotted.

add.legend

logical or integer, if TRUE or larger than zero then a legend with the tree names will be drawn.

object

object of class QualTreeSet.

...

optional arguments to be passed to plotAffyRNAdeg.

Value

AffyRNAdeg returns a list with following components:

N

number of probesets with identical number of probes

sample.names

names of samples, derived from affy batch object

mns

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

Since probes within a probeset are ordered directionally from the 5' end to the 3' end, it is possible to estimate the quality (degradation status) of the RNA.

Function AffyRNAdeg averages the probe intensities by location in the probeset, with the average taken over all probesets with identical number of probes.

Function summaryAffyRNAdeg produces a single summary statistic for each array.

Function plotAffyRNAdeg produces a side-by-side plot of the averaged intensities. Option transform = "none" shows the averaged intensities for each array while option "shift" staggers the plots for individual arrays vertically to make the display easier to read, and option "scale" normalizes the averaged intensities so that the standard deviation is equal to one.

Setting parameter add.legend = TRUE will add a legend containing all tree names to the plot, while setting e.g. add.legend = 6 will only show the first 6 tree names.

Examples

## Not run: 
# rnadeg <- xpsRNAdeg(rlm.all, treename="*", qualopt="raw")
# plotAffyRNAdeg(rnadeg)
# 
# rnadeg <- AffyRNAdeg(rlm.all)
# result <- summaryAffyRNAdeg(rnadeg)
# 
# ## plot RNA degradation
# plotAffyRNAdeg(rnadeg)
# 
# ## plot slope of RNA degradation
# plotAffyRNAdeg(rnadeg, summary = TRUE)
# ## End(Not run)