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IsoGene (version 1.0-24)

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.

See Also

IsoGene1

Examples

Run this code
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")

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