affy (version 1.50.0)

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.

See Also

mva.pairs

Examples

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