rleplot-methods: Box Plots of 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.

Usage

rleplot(x, which = "UnitName", size = 0, range = 0, names = "namepart", main = "RLE Plot", ylim = c(-1.0, 1.0), las = 2, add.line = TRUE, outline = FALSE, ...)

Arguments

x	object of class ExprTreeSet or QualTreeSet.
which	type of probes to be used, for details see validData.
size	length of sequence to be generated as subset.
range	determines how far the plot whiskers extend out from the box.
names	optional vector of sample names.
main	the main title for the plot.
ylim	range for the plotted y values.
las	the style of axis labels.
add.line	logical, if TRUE a horizontal line is drawn.
outline	if outline is not true, the outliers are not drawn.
...	optional arguments to be passed to boxplot.

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.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as boxplot.

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

Author(s)

Christian Stratowa

See Also

RLE, plotRLE, mboxplot, nuseplot

Examples

# load existing ROOT scheme file and ROOT expression file for rma
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.rma <- root.expr(scheme.test3, paste(path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/"), "mdp")

if (interactive()) {
rleplot(data.rma)
}

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