affy: mva.pairs – R documentation

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mva.pairs

M vs. A Matrix

Description

A matrix of M vs. A plots is produced. Plots are made on the upper triangle and the IQR of the Ms are displayed in the lower triangle

Usage

mva.pairs(x, labels=colnames(x), log.it=TRUE,span=2/3,family.loess="gaussian",
          digits=3,line.col=2,main="MVA plot",cex=2,...)

Arguments

`x`	a matrix containing the chip data in the columns.
`labels`	the names of the variables.
`log.it`	logical. If `TRUE`, uses log scale.
`span`	span to be used for loess fit.
`family.loess`	`"gaussian"` or `"symmetric"` as in `loess`.
`digits`	number of digits to use in the display of IQR.
`line.col`	color of the loess line.
`main`	an overall title for the plot.
`cex`	size for text.
`...`	graphical parameters can be given as arguments to `mva.plot`

Examples

x <- matrix(rnorm(4000),1000,4)
    x[,1] <- x[,1]^2
    dimnames(x) <- list(NULL,c("chip 1","chip 2","chip 3","chip 4"))
    mva.pairs(x,log=FALSE,main="example")

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