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

1
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.

Note

This function calculates the five test statistics using the maxT procedure that is controlling the Family Wise Error Rate.

Author(s)

Lin et al.

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

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  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)