# Mixture model on the Variance for the analysis of gene expression data

## Documentation for package `varmixt' version 0.2-4

## Help Pages

A B C E F N P Q S V

## -- A --

apo.data.vm | Apo Data set

## -- B --

boxplotvm | Boxplot of mean log-intensity in each variance group
boxplotvm.g | Boxplot of mean log-intensity in each variance group

## -- C --

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

## -- E --

export.res | Format and export analysis results

## -- F --

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 --

n.genes | Number of genes in a gene expression data object

## -- P --

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

## -- Q --

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

## -- S --

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

## -- V --

vm.analysis | Variance mixture analysis on unpaired data
vm.analysis.paired | Variance mixture analysis on paired data