affy: MAplot – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

MAplot

Relative M vs. A plots

Description

Create boxplots of M or M vs A plots. Where M is determined relative to a specified chip or to a pseudo-median reference chip.

Usage

MAplot(object,...)
Mbox(object,...)
ma.plot(A, M, subset = sample(1:length(M), min(c(10000, length(M)))),
        show.statistics = TRUE, span = 2/3, family.loess = "gaussian",
        cex = 2, plot.method = c("normal","smoothScatter","add"),
        add.loess = TRUE, lwd = 1, lty = 1, loess.col = "red", ...)

Arguments

`object`	an `AffyBatch-class`.
`...`	additional parameters for the routine.
`A`	a vector to plot along the horizontal axis.
`M`	a vector to plot along vertical axis.
`subset`	a set of indices to use when drawing the loess curve.
`show.statistics`	logical. If TRUE, some summary statistics of the M values are drawn.
`span`	span to be used for loess fit.
`family.loess`	`"guassian"` or `"symmetric"` as in `loess`.
`cex`	size of text when writing summary statistics on plot.
`plot.method`	a string specifying how the plot is to be drawn. `"normal"` plots points, `"smoothScatter"` uses the `smoothScatter` function. Specifying `"add"` means that the MAplot should be added to the current plot.
`add.loess`	add a loess line to the plot.
`lwd`	width of loess line.
`lty`	line type for loess line.
`loess.col`	color for loess line.

Examples

if (require(affydata)) {
   data(Dilution)
   MAplot(Dilution)
   Mbox(Dilution)
}

affy

Methods for Affymetrix Oligonucleotide Arrays

v1.68.0

LGPL (>= 2.0)

Authors

Rafael A. Irizarry <rafa@ds.harvard.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang

Initial release