spkMA: MA Plots

In mccallm/spkTools: Methods for Spike-in Arrays

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)

mccallm/spkTools documentation built on May 7, 2019, 1:26 p.m.