AffyRNAdeg: Functions to assess RNA Degradation.
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Author(s) Examples

Functions to detect possible RNA degradation.

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, ...)

`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`.

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.

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

Christian Stratowa, adapted from package affy

## 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)