The function calculates the pvalues using permutations under increasing and decreasing ordered alternatives for one gene. The pvalues (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 pvalues 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 Doseresponse Microarray Data in Early Drug Development Experiments Using R. Springer.
IsoGene: An R Package for Analyzing Doseresponse 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
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