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

Documentation for package ‘varmixt’ version 0.2-4

Help Pages

-- A --

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 --

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 --

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