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

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Documentation for package ‘varmixt’ version 0.2-4

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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