aroma.affymetrix (version 3.2.2)

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

# S3 method for 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)

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns.

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.

Author

Henrik Bengtsson

See Also

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