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aroma.affymetrix (version 3.0.0)

plotMvsX.AffymetrixCelFile: Plots log-ratio versus another variable in a scatter plot

Description

Plots log-ratio versus another variable in a scatter plot.

Usage

"plotMvsX"(this, reference, x, indices=NULL, pch=176, ylim=c(-1, 1) * 2, ylab=NULL, ..., what=c("M", "A"), add=FALSE, annotate=!add)

Arguments

reference
The reference channel, i.e. the denominator in the log ratios.
x
The other variable. A double vector.
indices
Indices of the probe signals to be plotted.
pch
The plot symbol.
xlim,ylim
The range of the x and the y axes.
xlab,ylab
The labels on the x and the y axes.
...
Additional arguments passed to plot.
annotate
If TRUE, the plot is annotated with information about the data plotted, otherwise not.

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns, and remaining data in the following columns.

See Also

*plotMvsA(). *smoothScatterMvsA(). For more information see AffymetrixCelFile.