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.

1 2 3 4 5 6 7 8 9 10 | ```
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)
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.