Manual for the R gaga package

Here we illustrate several uses of the package gaga, including simulation, differential expression analysis, class prediction and sample size calculations. In Section 1 we review the GaGa and MiGaGa models. In Section 2 we simulate gene expression data, which we use to fit the GaGa model in Section 3. Diagnostics for model goodness-of-fit are presented in Section 4. Section 5 shows how to find differentially expressed genes, Section 6 how to obtain fold change estimates and Section 7 how to classify samples into groups. Finally, in Section 8 we perform fixed and sequential sample size calculations.