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

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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

Description

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

Usage

## S3 method for class 'AffymetrixCelFile'
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.

Author(s)

Henrik Bengtsson

See Also

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

aroma.affymetrix documentation built on Aug. 21, 2025, 5:30 p.m.