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aroma.affymetrix (version 3.0.0)

smoothScatterMvsA.AffymetrixCelFile: Plots log-ratio versus log-intensity in a smooth scatter plot

Description

Plots log-ratio versus log-intensity in a smooth scatter plot.

Usage

"smoothScatterMvsA"(this, reference, indices=NULL, pch=176, xlim=c(0, 16), ylim=c(-1, 1) * diff(xlim), xlab=expression(A == 1/2 %*% log[2](y[1] * y[2])), ylab=expression(M == log[2](y[1]/y[2])), ..., annotate=TRUE)

Arguments

reference
The reference channel, i.e. the denominator in the log ratios.
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.

See Also

*plotMvsA(). Internally smoothScatter is used. For more information see AffymetrixCelFile.