ROKU                    detect tissue-specific (or tissue-selective)
                        patterns from microarray data with many kinds
                        of samples
TCC                     A package for differential expression analysis
                        from tag count data with robust normalization
                        strategies
TCC-class               A container for storing information used in TCC
WAD                     Calculate WAD statistic for individual genes
arab                    Arabidopsis RNA-Seq data set
calcAUCValue            Calculate AUC value from a TCC-class object
calcNormFactors         Calculate normalization factors
clusterSample           Perform hierarchical clustering for samples
                        from expression data
estimateDE              Estimate degrees of differential expression
                        (DE) for individual genes
filterLowCountGenes     Filter genes from a TCC-class object
getNormalizedData       Obtain normalized count data
getResult               Obtain the summaries of results after the
                        differential expression analysis
hypoData                A simulation dataset for comparing two-group
                        tag count data, focusing on RNA-seq
hypoData_mg             A simulation dataset for comparing three-group
                        tag count data, focusing on RNA-seq
hypoData_ts             A sample microarray data for detecting
                        tissue-specific patterns.
makeFCMatrix            Generate the fold change matrix for simulating
                        count data
nakai                   DNA microarray data set
plot                    Plot a log fold-change versus log average
                        expression (so-called M-A plot)
plotFCPseudocolor       Create a pseudo-color image of simulation data
simulateReadCounts      Generate simulation data from negative binomial
                        (NB) distribution
