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

smoothScatterMvsA.AffymetrixCelFileR Documentation

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.


HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.