RLE: Relative Log Expression (RLE)

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Produce boxplots of Relative Log Expression (RLE) values for the set of arrays. Alternatively, summary statistics or RLE values can be extracted as data.frame.

Usage

RLE(x, treename = "*", type = c("plot", "stats", "values"), qualopt = NULL, ...)

Arguments

x	object of class QualTreeSet.
treename	vector of tree names to export.
type	type of output, plot, stats or values.
qualopt	quality control option, i.e. ‘raw’, ‘adjusted’, ‘normalized’ or ‘all’.
...	optional arguments to be passed to rleplot.

Details

Create boxplots of Relative Log Expression (RLE) values for the set of arrays, i.e. of M plots, where M is determined relative to a pseudo-median reference chip.

Alternatively it is possible to extract either the summary statistics as data.frame (type="stats") or all RLE values as data.frame (type="values").

If an object of class QualTreeSet was created by fitting a probe level model with qualopt="all" then RLE will plot or extract RLE for "all" quality options. If you want to plot or extract RLE for a certain quality option only, e.g. "normalized" data only, then you can use parameter qualopt with qualopt="<qualopt>".

Author(s)

Christian Stratowa

See Also

plotRLE, rleplot

Examples

## Not run: 
## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## qualification - rlm
rlm.all <- rmaPLM(data.test3, "tmp_Test3RLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", add.data=FALSE)

## plot expression levels
if (interactive()) {
RLE(rlm.all)
RLE(rlm.all, qualopt="normalized")
qcRLE <- RLE(rlm.all, type="stats")
qcRLE <- RLE(rlm.all, type="values")
qcRLE <- RLE(rlm.all, treename="TestA1_normalized.rlm", type="stats")
qcRLE <- RLE(rlm.all, treename="TestA1_normalized.rlm", type="values")
}

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.