boxplot-methods: boxplot of a ExpressionSet object

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

Creating boxplot of sample intensities in a ExpressionSet object

Usage

## S4 method for signature 'ExpressionSet'
boxplot(x, range = 0, main, logMode = TRUE, subset = NULL, xlab = "", ylab = "Amplitude", ...)

Arguments

x	a ExpressionSet object
range	parameter of boxplot
main	title of the boxplot
logMode	whether plot the data in log2 scale or not
subset	subset of rows used to plot. It can be an index vector, or the length of a random subset
xlab	xlab of the plot
ylab	ylab of the plot
...	optional arguments to boxplot.

Details

The boxplot function has a "subset" parameter. By default, it is set as 5000, i.e., randomly selected 5000 probes to plot the boxplot. The purpose of this is to plot the picture faster, but it will also make the boxplot has slightly different each time. If the user wants to make sure the boxplot is the same each time, you can set the "subset" parameter as NULL.

See Also

LumiBatch-class, boxplot and boxplot,MethyLumiM-method

Examples

## load example data
data(example.lumi)

boxplot(example.lumi)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.