aroma.affymetrix (version 3.2.2)

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

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns, and remaining data in the following columns.

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.

Author

Henrik Bengtsson

See Also

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