# IsoGene v1.0-24

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## Order-Restricted Inference for Microarray Experiments

Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.

## Functions in IsoGene

 Name Description IsomaxT The maxT procedure for order restricted inference Isoallfdr Obtaining the delta table in the SAM procedure IsoGenemSAM The five SAM test statistics calculated for both the increasing and decreasing trends IsoGenem The five test statistics calculated for both the increasing and decreasing trends exampleData Dose-response microarray example data dopamine Dose-response microarray example data IsoGene1 The five test statistics calculated for both the increasing and decreasing trends IsoBHPlot Plot of adjusted p-values using BH or BY adjustment Isofudge Calculation of the fudge factor for the five SAM test statistics in the SAM procedure IsoGene-package IsoGene Isoqqstat Implementation of five SAM test statistics in the SAM procedure IsoTestBH Test of monotonic trends using the five test statistics with BH or BY adjustment IsopvaluePlot Plot of p-values from permutations under increasing or decreasing alternatives IsoSAMPlot Plots produced using the SAM procedure Isoqval Obtaining the list of significant genes using the SAM procedure IsoTestSAM Obtaining the list of significant genes using the SAM procedure IsoPlot IsoPlot IsoRawp IsoRawp No Results!