plot.ratioScatter: Plot ratios of all possible combinations of IP and CONTROL
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Author(s) See Also Examples

A matrix of pairwise scatterplots of the ratios is created. The lower panel shows the correlation of the data.

1	plotRatioScatter(eSet, ip, control, density=F, sample=NULL, cluster=T, cex=1)

`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
`density`	if TRUE, a density scatter plot is plotted. This plot shows the density of the data.
`sample`	An integer, indicating the number of subsamples to take for the density scatterplot. This is only recommended if the data is very large, as the density computation takes some time.

`cluster`	if cluster=T, the experiments are clustered and similiar experiments are plotted together.
`cex`	see ?par

Benedikt Zacher zacher@lmb.uni-muenchen.de

pairs, densityscatter

##
points <- 10^4
x <- rnorm(points/2)
x <- c(x,x+2.5)
x <- sign(x)*abs(x)^1.3
y <- x + rnorm(points,sd=0.8)
z <- y*2
mat <- matrix(c(x,y,z), ncol=3)
colnames(mat) <- c("A", "B1", "B2")
plotRatioScatter(mat, c(TRUE, FALSE, FALSE), c(FALSE, TRUE, TRUE), density=TRUE)