8 research outputs found
Simultaneous confidence intervals that are compatible with closed testing in adaptive designs
We describe a general method for finding a confidence region for a parameter vector that is compatible with the decisions of a two-stage closed test procedure in an adaptive experiment. The closed test procedure is characterized by the fact that rejection or nonrejection of a null hypothesis may depend on the decisions for other hypotheses and the compatible confidence region will, in general, have a complex, nonrectangular shape. We find the smallest cross-product of simultaneous confidence intervals containing the region and provide computational shortcuts for calculating the lower bounds on parameters corresponding to the rejected null hypotheses. We illustrate the method with an adaptive phase II/III clinical trial
IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R
The analysis of transcriptomic experiments with ordered covariates, such as dose-response
data, has become a central topic in bioinformatics, in particular in omics studies. Consequently,
multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various
perspectives under the assumption of order restriction. We introduce the new R package IsoGene
Graphical User Interface (IsoGeneGUI), an extension of the original IsoGene package that includes
methods from most of available R packages designed for the analysis of order restricted microarray
data, namely orQA, ORIClust, goric and ORCME. The methods included in the new IsoGeneGUI
range from inference and estimation to model selection and clustering tools. The IsoGeneGUI is not
only the most complete tool for the analysis of order restricted microarray experiments available in
R but also it can be used to analyse other types of dose-response data. The package provides all the
methods in a user friendly fashion, so analyses can be implemented by users with limited knowledge
of R programming