IsopvaluePlot: Plot of p-values from permutations under increasing or decreasing alternatives
Description
The function calculates the p-values using permutations under increasing
and decreasing ordered alternatives for one gene. The p-values ($p^up$ and
$p^down$) are obtained from the plot of null distribution and observed statistics.
Usage
IsopvaluePlot(x, y, niter, stat = c("E2", "Williams", "Marcus", "M", "ModifM"))
Arguments
x
the dose levels
y
the gene expressions
niter
the number of permutations to use
stat
choose one of the five test statistics to use
Value
Plots of the null distribution and the observed test statistic under
increasing and decreasing ordered alternatives.
References
Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens,
L. (editors). (2012) Modeling Dose-response Microarray
Data in Early Drug Development Experiments Using
R. Springer.
IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2/1.
x <- c(rep(1,3), rep(2,3), rep(3,3), rep(4,3))
y <- c(rnorm(3,1,1), rnorm(3,2,1), rnorm(3,3,1), rnorm(3,4,1))
IsopvaluePlot(x, y, niter = 1000, stat = "Williams")