apo.data.vm             Apo Data set
boxplotvm               Boxplot of mean log-intensity in each variance
                        group
boxplotvm.g             Boxplot of mean log-intensity in each variance
                        group
compare.method          Compare the different analysis methods
compare.res             Compare the results from 2 analysis
compare.var             How to compare variance in the 2 conditions
export.res              Format and export analysis results
fdr.an                  FDR analysis of variance mixture analysis
                        results
fdr.compare.method      Comparison of the different analysis methods
fdr.compare.res         Comparison of the results from 2 analysis
find.qval.index         Subset of genes based on Q value
n.genes                 Number of genes in a gene expression data
                        object
plotrm                  Plot of mean log-ratio versus mean
                        log-intensity
plotsdt                 Plot Test statistic versus denominator of test
                        statistic
plotsdt.VM              Plot of VM test statistic versus denominator
plotvm                  Plot of log-variance versus mean intensity
pval.an                 Number of regulated genes
qplot.vm                Plot Diagnostic of FDR computation
qqplot.var.vm           QQ plot of the distribution of estimated
                        variance
qqplot.var.vm.2         QQ plot of the variance versus gamma
                        distribution in one variance group
qqplot.vm               QQ plot of the residuals
qval.VM.vect            Vector of VM q-values from vm.result data
                        object
qval.VM2.vect           Vector of VM2 q-values from vm.result data
                        object
qval.anova.vect         Vector of homoscedastic q-values from vm.result
                        data object
qval.gene.vect          Vector of gene specific q-values from vm.result
                        data object
sbset.gene              Subset of vm.result object using gene IDs
sbset.pval              Subset of vm.result object using gene p-values
sbset.qval              Subset of vm.result object using gene q-values
sd.param                Standard deviation of the variance mixture
                        model parameters
spleen.data.vm          Spleen Data set
vm.analysis             Variance mixture analysis on unpaired data
vm.analysis.paired      Variance mixture analysis on paired data
