MAplot of a ExpressionSet object

Description

Creating pairwise MAplot of sample intensities in a ExpressionSet object

Usage

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## 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

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## load example data
data(example.lumi)

MAplot(example.lumi)

MAplot(example.lumi, smoothScatter=TRUE)

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