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

In HenrikBengtsson/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.

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