spkTools (version 1.28.0)

spkMA: 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.

Examples

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