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

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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.

Note

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

Author(s)

Lin et al.

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.

See Also

IsoGene1

Examples

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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")