IsoGene (version 1.0-24)

IsomaxT: The maxT procedure for order restricted inference

Description

The function calculates the adjusted p-values for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M) using the maxT procedure.

Usage

IsomaxT(x, y, niter)

Arguments

x

indicates the dose levels

y

a data frame of the gene expression

niter

number of permutations to use

Value

A matrix with adjusted p-values for the five test statistics.

References

Resampling based multiple testing, Westfall, P.H. and Young, S.S. 1993, Willy.

Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R, Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors), (2012), Springer.

See Also

IsoTestBH

Examples

 
  x.res <- c(rep(1,3),rep(2,3),rep(3,3))
  y1 <- matrix(rnorm(90, 1,1),10,9)  # 10 genes with no trends
  y2 <- matrix(c(rnorm(30, 1,1), rnorm(30,2,1),
                 rnorm(30,3,1)), 10, 9)  # 10 genes with increasing trends
  dat.mat <- data.frame(rbind(y1, y2))  # y needs to be a data frame  
  niter=1000 
  
  set.seed(1234)
  pval.maxT <- IsomaxT(x.res, dat.mat,niter)