plotMvsX.AffymetrixCelFile: Plots log-ratio versus another variable in a scatter plot

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

Plots log-ratio versus another variable in a scatter plot

Description

Plots log-ratio versus another variable in a scatter plot.

Usage

## S3 method for class 'AffymetrixCelFile'
plotMvsX(this, reference, x, indices=NULL, pch=176, ylim=c(-1, 1) * 2, ylab=NULL, ...,
  what=c("M", "A"), add=FALSE, annotate=!add)

Arguments

reference	The reference channel, i.e. the denominator in the log ratios.
x	The other variable. A double vector.
indices	Indices of the probe signals to be plotted.
pch	The plot symbol.
ylim	The range of the y axes.
ylab	The labels on 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, and remaining data in the following columns.

Author(s)

Henrik Bengtsson

See Also

*plotMvsA(). *smoothScatterMvsA(). For more information see AffymetrixCelFile.

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