IsomaxT: The maxT procedure for order restricted inference
In IsoGene: Order-Restricted Inference for Microarray Experiments

Description Usage Arguments Value Note Author(s) References See Also Examples

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.

1	IsomaxT(x, y, niter)

`x`	indicates the dose levels
`y`	a data frame of the gene expression
`niter`	number of permutations to use

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

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

Lin et al.

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.

IsoTestBH

 
  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)