plotEffectSize {SSPA}R Documentation

Plots the density of effect sizes of the pilot data

Description

The function plotEffectSize plots density of effect sizes of the pilot data.

Usage

plotEffectSize(x, threshold = 0, xlab = "effect size", ylab = "density of effect sizes", main, sub, ...)

Arguments

x object of class SampleSize-class
threshold threshold for truncation of the density of effect-sizes. The threshold will be taken symmetrical around the y-axis.
xlab a title for the x axis
ylab a title for the y axis
main an overall title for the plot
sub a sub title for the plot
... additional arguments given to plot or par

Details

The density of effect sizes describes the effects observed in the pilot data. Usually a bimodal density is observed representing up- and down-regulated genes. The way in which the test statistics is calculated determines what is meant by up- and down-regulation. A small symmetrical region around zero can be defined that will be excluded from the density of effect sizes and thereby increases the estimated average power.

References

Ferreira, F.A., Zwinderman, A., (2006). Approximate Power and Sample Size Calculations with Microarray Data: An Illustration. Statistical Applications in Genetics and Molecular Biology 5, (1).

Examples

library(multtest)
data(golub)
teststat <- mt.teststat(golub, golub.cl)
table(golub.cl)
pd <- pilotData(name="golub", testStatistics=teststat, sampleSizeA=11, sampleSizeB=27)
hist(pd)
plot(pd)
ss <- sampleSize(pd)
plotEffectSize(ss)

[Package SSPA version 1.0.0 Index]