MAplot-methods: MAplot of a ExpressionSet object

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

Description

Creating pairwise MAplot of sample intensities in a ExpressionSet object

Usage

## S4 method for signature 'ExpressionSet'
MAplot(object, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, main = NULL)

Arguments

object	an ExpressionSet object
...	optional arguments to MAplot.
smoothScatter	whether use smoothScatter function to plot points
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
main	title of the plot

Details

To increase the plot efficiency, by default, we only plot RANDOMLY selected subset of points (based on parameter "subset"). If users want to plot all the points, they can set the parameter "subset = NULL". When smoothScatter is set as TRUE, the subsetting will be suppressed because smoothScatter function has good plot efficiency for large number of points.

See Also

LumiBatch-class, MAplot

Examples

## load example data
data(example.lumi)

MAplot(example.lumi)

MAplot(example.lumi, smoothScatter=TRUE)

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