spkMA {spkTools}R Documentation

MA Plots

Description

Plots log-ratios (M) vs. average log expression (A) for a SpikeInExpressionSet object.

Usage

spkMA(object, spkSlopeOut, fc=2, tol=3, label=NULL, ylim=NULL,
outlier=1, reduce=TRUE, plot.legend=TRUE)

Arguments

object a SpikeInExpressionSet object
spkSlopeOut the output from the spkSlope function
fc the fold change of interest
tol the precision (number of digits after decimal point) in fc
label a character string to insert into the plot title
ylim limits of y-axis
outlier log fold change cut-off for outliers
reduce if TRUE some points are removed from the background to speed plotting
plot.legend if TRUE a legend is plotted

Value

The MA plot is produced.

Author(s)

Matthew N. McCall

Examples

data(affy)
affySlope <- spkSlope(affy)
spkMA(affy, affySlope)

[Package spkTools version 1.0.0 Index]