MAplot {affy} | R Documentation |
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)
}
[Package
affy version 1.28.0
Index]