plot.ma: M versus A plot
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Author(s) See Also Examples

A matrix of M vs. A plots of each pair (ip, control) is produced.

1	plotMA(eSet, ip=NULL, control=NULL, col=NULL)

`eSet`	an ExprssionSet or matrix, containing the data
`ip`	an integer, or boolean vector, that indicates, which columns in the ExpressionSet are IP experiments
`control`	an integer, or boolean vector, that indicates, which columns in the ExpressionSet are CONTROL or REFERENCE experiments
`col`	color, to fill the boxes

Benedikt Zacher zacher@lmb.uni-muenchen.de

ma.plot

##
mat <- matrix(rnorm(1000000), ncol=4)
colnames(mat) <- c("Sample1", "Sample2", "Sample3", "Sample4")
mat[,1] <- mat[,1]^2
plotMA(mat, c(TRUE, FALSE, TRUE, FALSE), c(FALSE, TRUE, FALSE, TRUE))