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| 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.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 |
| 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 |
| 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 |