IsopvaluePlot: Plot of p-values from permutations under increasing or...
In IsoGene: Order-Restricted Inference for Microarray Experiments

Description Usage Arguments Value Note Author(s) References See Also Examples

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.

1	IsopvaluePlot(x, y, niter, stat = c("E2", "Williams", "Marcus", "M", "ModifM"))

`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

Plots of the null distribution and the observed test statistic under increasing and decreasing ordered alternatives.

The function obtains the p-values under increasing and decreasing ordered alternatives for a single gene.

Lin et al.

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.

IsoGene1

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")