Entry: apo.data.vm
Aliases: apo.data.vm
Keywords: datasets
Description: Apo Data set
URL: ../../../library/varmixt/html/apo.data.vm.html

Entry: badqual.mat
Aliases: badqual.mat
Keywords: internal
Description: How to get bad quality matrix
URL: ../../../library/varmixt/html/badqual.mat.html

Entry: block.vect
Aliases: block.vect
Keywords: internal
Description: Extraction of the block information vector
URL: ../../../library/varmixt/html/block.vect.html

Entry: boxplotvm
Aliases: boxplotvm
Keywords: htest
Description: Boxplot of mean log-intensity in each variance group
URL: ../../../library/varmixt/html/boxplotvm.html

Entry: boxplotvm.g
Aliases: boxplotvm.g
Keywords: htest
Description: Boxplot of mean log-intensity in each variance group
URL: ../../../library/varmixt/html/boxplotvm.g.html

Entry: build.data
Aliases: build.data
Keywords: internal
Description: How to build gene expression data object wiht unpaired data
URL: ../../../library/varmixt/html/build.data.html

Entry: build.data.paired
Aliases: build.data.paired
Keywords: internal
Description: How to build a gene expression data object with paired data
URL: ../../../library/varmixt/html/build.data.paired.html

Entry: choose.nmixt
Aliases: choose.nmixt
Keywords: internal
Description: Fow to choose the number of components in the mixture model
URL: ../../../library/varmixt/html/choose.nmixt.html

Entry: choose.nmixt.VM
Aliases: choose.nmixt.VM
Keywords: internal
Description: How to choose the number of components of the mixture model
URL: ../../../library/varmixt/html/choose.nmixt.VM.html

Entry: comp.bic.2
Aliases: comp.bic.2
Keywords: internal
Description: Study of the evolution of log-likelihood
URL: ../../../library/varmixt/html/comp.bic.2.html

Entry: comp.bic
Aliases: comp.bic
Keywords: internal
Description: BIC and AIC criteria
URL: ../../../library/varmixt/html/comp.bic.html

Entry: comp.bic.stoch
Aliases: comp.bic.stoch
Keywords: internal
Description: Computes mixture parameters for varying number of components
URL: ../../../library/varmixt/html/comp.bic.stoch.html

Entry: compare.method
Aliases: compare.method
Keywords: htest
Description: Compare the different analysis methods
URL: ../../../library/varmixt/html/compare.method.html

Entry: compare.res
Aliases: compare.res
Keywords: htest
Description: Compare the results from 2 analysis
URL: ../../../library/varmixt/html/compare.res.html

Entry: compare.var
Aliases: compare.var
Keywords: htest
Description: How to compare variance in the 2 conditions
URL: ../../../library/varmixt/html/compare.var.html

Entry: compute.BIC
Aliases: compute.BIC
Keywords: internal
Description: Computation of the parameters of the mixture with deterministic initial parameters
URL: ../../../library/varmixt/html/compute.BIC.html

Entry: compute.BIC.init
Aliases: compute.BIC.init
Keywords: internal
Description: Computation of parameters of the mixture model given initial parameters
URL: ../../../library/varmixt/html/compute.BIC.init.html

Entry: compute.BIC.stoch
Aliases: compute.BIC.stoch
Keywords: internal
Description: Computes parameters of the mixture on the variance with EM algorithm with random initial parameters
URL: ../../../library/varmixt/html/compute.BIC.stoch.html

Entry: compute.P3
Aliases: compute.P3
Keywords: internal
Description: Internal Function for computing P-value in variance mixture model
URL: ../../../library/varmixt/html/compute.P3.html

Entry: compute.dif
Aliases: compute.dif
Keywords: internal
Description: Function to compute simple statistics with unpaired data
URL: ../../../library/varmixt/html/compute.dif.html

Entry: compute.dif.paired
Aliases: compute.dif.paired
Keywords: internal
Description: Function to compute simple statistics with paired data
URL: ../../../library/varmixt/html/compute.dif.paired.html

Entry: compute.param
Aliases: compute.param
Keywords: internal
Description: Computes the mixture parameters
URL: ../../../library/varmixt/html/compute.param.html

Entry: compute.param.VM
Aliases: compute.param.VM
Keywords: internal
Description: Computes the parameters given the number of components in the model
URL: ../../../library/varmixt/html/compute.param.VM.html

Entry: cond1.mat
Aliases: cond1.mat
Keywords: internal
Description: Extraction of the matrix with normalized expression data in condition 1
URL: ../../../library/varmixt/html/cond1.mat.html

Entry: cond2.mat
Aliases: cond2.mat
Keywords: internal
Description: Extraction of the matrix with normalized expression data in condition 2
URL: ../../../library/varmixt/html/cond2.mat.html

Entry: df.vect
Aliases: df.vect
Keywords: internal
Description: Number of degrees of freedom used in the variance estimation
URL: ../../../library/varmixt/html/df.vect.html

Entry: dif.f
Aliases: dif.f
Keywords: internal
Description: Intermediary function
URL: ../../../library/varmixt/html/dif.f.html

Entry: export.res
Aliases: export.res
Keywords: htest
Description: Format and export analysis results
URL: ../../../library/varmixt/html/export.res.html

Entry: fdr
Aliases: fdr
Keywords: internal
Description: Computation of FDR from a vector of P-value
URL: ../../../library/varmixt/html/fdr.html

Entry: fdr.an
Aliases: fdr.an
Keywords: htest
Description: FDR analysis of variance mixture analysis results
URL: ../../../library/varmixt/html/fdr.an.html

Entry: fdr.compare.method
Aliases: fdr.compare.method
Keywords: htest
Description: Comparison of the different analysis methods
URL: ../../../library/varmixt/html/fdr.compare.method.html

Entry: fdr.compare.res
Aliases: fdr.compare.res
Keywords: htest
Description: Comparison of the results from 2 analysis
URL: ../../../library/varmixt/html/fdr.compare.res.html

Entry: fdr.nmatch.an
Aliases: fdr.nmatch.an
Keywords: internal
Description: Match result for varmixt model
URL: ../../../library/varmixt/html/fdr.nmatch.an.html

Entry: fdr.nmatch.an.anova
Aliases: fdr.nmatch.an.anova
Keywords: internal
Description: Match result for homoscedastic model
URL: ../../../library/varmixt/html/fdr.nmatch.an.anova.html

Entry: fdr.nmatch.an.gene
Aliases: fdr.nmatch.an.gene
Keywords: internal
Description: Match result for gene-specific model
URL: ../../../library/varmixt/html/fdr.nmatch.an.gene.html

Entry: find.gene.index
Aliases: find.gene.index
Keywords: internal
Description: Indexes of a vector of gene IDs
URL: ../../../library/varmixt/html/find.gene.index.html

Entry: find.pval.index
Aliases: find.pval.index
Keywords: internal
Description: Index of genes below using p-value criterion
URL: ../../../library/varmixt/html/find.pval.index.html

Entry: find.qval.index
Aliases: find.qval.index
Keywords: htest
Description: Subset of genes based on Q value
URL: ../../../library/varmixt/html/find.qval.index.html

Entry: gene.anot.data.frame
Aliases: gene.anot.data.frame
Keywords: internal
Description: Gene anotation data frame
URL: ../../../library/varmixt/html/gene.anot.data.frame.html

Entry: gene.id.vect
Aliases: gene.id.vect
Keywords: internal
Description: Extraction of a vector with the name of each gene
URL: ../../../library/varmixt/html/gene.id.vect.html

Entry: geneid.vect
Aliases: geneid.vect
Keywords: internal
Description: Extraction of a vector with the name of each gene
URL: ../../../library/varmixt/html/geneid.vect.html

Entry: get.sas.export
Aliases: get.sas.export
Keywords: internal
Description: get.sas.export
URL: ../../../library/varmixt/html/get.sas.export.html

Entry: group.vect
Aliases: group.vect
Keywords: internal
Description: Extraction of the vector of the variance group of each gene
URL: ../../../library/varmixt/html/group.vect.html

Entry: histresid.vm
Aliases: histresid.vm
Keywords: internal
Description: histresid.vm
URL: ../../../library/varmixt/html/histresid.vm.html

Entry: histvm
Aliases: histvm
Keywords: internal
Description: histvm
URL: ../../../library/varmixt/html/histvm.html

Entry: keep.index
Aliases: keep.index
Keywords: internal
Description: Subset of vm.result data object based on index
URL: ../../../library/varmixt/html/keep.index.html

Entry: logratio.mat
Aliases: logratio.mat
Keywords: internal
Description: Matrix of normalized log-ratio
URL: ../../../library/varmixt/html/logratio.mat.html

Entry: logratio.vect
Aliases: logratio.vect
Keywords: internal
Description: Vector of mean log-ratio
URL: ../../../library/varmixt/html/logratio.vect.html

Entry: make.param
Aliases: make.param
Keywords: internal
Description: A function to build a parameter object
URL: ../../../library/varmixt/html/make.param.html

Entry: meanint.mat
Aliases: meanint.mat
Keywords: internal
Description: Matrix of gene mean intensity
URL: ../../../library/varmixt/html/meanint.mat.html

Entry: meanint.vect
Aliases: meanint.vect
Keywords: internal
Description: Vector of mean gene intensity
URL: ../../../library/varmixt/html/meanint.vect.html

Entry: n.genes
Aliases: n.genes
Keywords: htest
Description: Number of genes in a gene expression data object
URL: ../../../library/varmixt/html/n.genes.html

Entry: n.mixt
Aliases: n.mixt
Keywords: internal
Description: Number of mixture components in the model
URL: ../../../library/varmixt/html/n.mixt.html

Entry: nmatch.an
Aliases: nmatch.an
Keywords: internal
Description: Match results for Varmixt model
URL: ../../../library/varmixt/html/nmatch.an.html

Entry: nmatch.an.anova
Aliases: nmatch.an.anova
Keywords: internal
Description: Match result for homoscedastic model
URL: ../../../library/varmixt/html/nmatch.an.anova.html

Entry: nmatch.an.gene
Aliases: nmatch.an.gene
Keywords: internal
Description: Match result for gene-specific model
URL: ../../../library/varmixt/html/nmatch.an.gene.html

Entry: normalize.data
Aliases: normalize.data
Keywords: internal
Description: Data Normalization
URL: ../../../library/varmixt/html/normalize.data.html

Entry: normalize.data.paired
Aliases: normalize.data.paired
Keywords: internal
Description: Data normalization
URL: ../../../library/varmixt/html/normalize.data.paired.html

Entry: parameters.data.frame
Aliases: parameters.data.frame
Keywords: internal
Description: Data.frame with the variance mixture model parameters
URL: ../../../library/varmixt/html/parameters.data.frame.html

Entry: plotrm
Aliases: plotrm
Keywords: htest
Description: Plot of mean log-ratio versus mean log-intensity
URL: ../../../library/varmixt/html/plotrm.html

Entry: plotsdm
Aliases: plotsdm
Keywords: internal
Description: plotsdm
URL: ../../../library/varmixt/html/plotsdm.html

Entry: plotsdt
Aliases: plotsdt
Keywords: htest
Description: Plot Test statistic versus denominator of test statistic
URL: ../../../library/varmixt/html/plotsdt.html

Entry: plotsdt.VM
Aliases: plotsdt.VM
Keywords: htest
Description: Plot of VM test statistic versus denominator
URL: ../../../library/varmixt/html/plotsdt.VM.html

Entry: plotvm
Aliases: plotvm
Keywords: htest
Description: Plot of log-variance versus mean intensity
URL: ../../../library/varmixt/html/plotvm.html

Entry: prt.varmixt.res
Aliases: prt.varmixt.res
Keywords: internal
Description: Parameters of varmixt analysis
URL: ../../../library/varmixt/html/prt.varmixt.res.html

Entry: pval.VM.corrected.vect
Aliases: pval.VM.corrected.vect
Keywords: internal
Description: Bonferroni corrected p-value from "continuous" mixture model (without assignment)
URL: ../../../library/varmixt/html/pval.VM.corrected.vect.html

Entry: pval.VM.vect
Aliases: pval.VM.vect
Keywords: internal
Description: p-value from "continuous" mixture model (without assignment)
URL: ../../../library/varmixt/html/pval.VM.vect.html

Entry: pval.VM2.corrected.vect
Aliases: pval.VM2.corrected.vect
Keywords: internal
Description: Vector of corrected (Sidak) p-value from variance mixture model
URL: ../../../library/varmixt/html/pval.VM2.corrected.vect.html

Entry: pval.VM2.vect
Aliases: pval.VM2.vect
Keywords: internal
Description: Vector of p-value from variance mixture model
URL: ../../../library/varmixt/html/pval.VM2.vect.html

Entry: pval.an
Aliases: pval.an
Keywords: htest
Description: Number of regulated genes
URL: ../../../library/varmixt/html/pval.an.html

Entry: pval.anova.corrected.vect
Aliases: pval.anova.corrected.vect
Keywords: internal
Description: Vector of corrected (Bonferroni) p-value from homoscedastic variance model
URL: ../../../library/varmixt/html/pval.anova.corrected.vect.html

Entry: pval.anova.vect
Aliases: pval.anova.vect
Keywords: internal
Description: Vector of p-value from homoscedastic variance model
URL: ../../../library/varmixt/html/pval.anova.vect.html

Entry: pval.gene.corrected.vect
Aliases: pval.gene.corrected.vect
Keywords: internal
Description: Vector of corrected (Sidak) p-value from gene-specific variance model
URL: ../../../library/varmixt/html/pval.gene.corrected.vect.html

Entry: pval.gene.vect
Aliases: pval.gene.vect
Keywords: internal
Description: Vector of p-value from gene-specific variance model
URL: ../../../library/varmixt/html/pval.gene.vect.html

Entry: qplot.vm
Aliases: qplot.vm
Keywords: htest
Description: Plot Diagnostic of FDR computation
URL: ../../../library/varmixt/html/qplot.vm.html

Entry: qqplot.gamma
Aliases: qqplot.gamma
Keywords: internal
Description: QQ plot of gamma distribution
URL: ../../../library/varmixt/html/qqplot.gamma.html

Entry: qqplot.var.vm.2
Aliases: qqplot.var.vm.2
Keywords: htest
Description: QQ plot of the variance versus gamma distribution in one variance group
URL: ../../../library/varmixt/html/qqplot.var.vm.2.html

Entry: qqplot.var.vm
Aliases: qqplot.var.vm
Keywords: htest
Description: QQ plot of the distribution of estimated variance
URL: ../../../library/varmixt/html/qqplot.var.vm.html

Entry: qqplot.vm.2
Aliases: qqplot.vm.2
Keywords: internal
Description: qqplot.vm.2
URL: ../../../library/varmixt/html/qqplot.vm.2.html

Entry: qqplot.vm
Aliases: qqplot.vm
Keywords: htest
Description: QQ plot of the residuals
URL: ../../../library/varmixt/html/qqplot.vm.html

Entry: qual.vect
Aliases: qual.vect
Keywords: internal
Description: Vector with global quality info for each gene
URL: ../../../library/varmixt/html/qual.vect.html

Entry: quality.filter
Aliases: quality.filter
Keywords: internal
Description: Filter out genes with low quality observations
URL: ../../../library/varmixt/html/quality.filter.html

Entry: qval.VM.vect
Aliases: qval.VM.vect
Keywords: htest
Description: Vector of VM q-values from vm.result data object
URL: ../../../library/varmixt/html/qval.VM.vect.html

Entry: qval.VM2.vect
Aliases: qval.VM2.vect
Keywords: htest
Description: Vector of VM2 q-values from vm.result data object
URL: ../../../library/varmixt/html/qval.VM2.vect.html

Entry: qval.anova.vect
Aliases: qval.anova.vect
Keywords: htest
Description: Vector of homoscedastic q-values from vm.result data object
URL: ../../../library/varmixt/html/qval.anova.vect.html

Entry: qval.gene.vect
Aliases: qval.gene.vect
Keywords: htest
Description: Vector of gene specific q-values from vm.result data object
URL: ../../../library/varmixt/html/qval.gene.vect.html

Entry: rank.VM2.vect
Aliases: rank.VM2.vect
Keywords: internal
Description: Vector of the ranks of each gene with variance mixture model
URL: ../../../library/varmixt/html/rank.VM2.vect.html

Entry: rank.anova.vect
Aliases: rank.anova.vect
Keywords: internal
Description: Vector of the ranks of each gene with homoscedastic variance model
URL: ../../../library/varmixt/html/rank.anova.vect.html

Entry: rank.gene.vect
Aliases: rank.gene.vect
Keywords: internal
Description: Vector of the ranks of each gene with gene-specific variance model
URL: ../../../library/varmixt/html/rank.gene.vect.html

Entry: raw.cond1.mat
Aliases: raw.cond1.mat
Keywords: internal
Description: Matrix of raw data in condition 1
URL: ../../../library/varmixt/html/raw.cond1.mat.html

Entry: raw.cond2.mat
Aliases: raw.cond2.mat
Keywords: internal
Description: Matrix of raw data in condition 2
URL: ../../../library/varmixt/html/raw.cond2.mat.html

Entry: raw.log.ratio.mat
Aliases: raw.log.ratio.mat
Keywords: internal
Description: Matrix of raw log-ratio
URL: ../../../library/varmixt/html/raw.log.ratio.mat.html

Entry: raw.meanint.mat
Aliases: raw.meanint.mat
Keywords: internal
Description: Matrix of raw mean log-intensity
URL: ../../../library/varmixt/html/raw.meanint.mat.html

Entry: remove.index
Aliases: remove.index
Keywords: internal
Description: Subset of vm.result object by removing index
URL: ../../../library/varmixt/html/remove.index.html

Entry: res.data.frame
Aliases: res.data.frame
Keywords: internal
Description: Dataframe with analysis results
URL: ../../../library/varmixt/html/res.data.frame.html

Entry: residual.mat
Aliases: residual.mat
Keywords: internal
Description: Matrix of residuals
URL: ../../../library/varmixt/html/residual.mat.html

Entry: sbset.gene
Aliases: sbset.gene
Keywords: htest
Description: Subset of vm.result object using gene IDs
URL: ../../../library/varmixt/html/sbset.gene.html

Entry: sbset.pval
Aliases: sbset.pval
Keywords: htest
Description: Subset of vm.result object using gene p-values
URL: ../../../library/varmixt/html/sbset.pval.html

Entry: sbset.qval
Aliases: sbset.qval
Keywords: htest
Description: Subset of vm.result object using gene q-values
URL: ../../../library/varmixt/html/sbset.qval.html

Entry: sd.delta.VM.vect
Aliases: sd.delta.VM.vect
Keywords: internal
Description: Standard deviation of the test statistic in the variance mixture model
URL: ../../../library/varmixt/html/sd.delta.VM.html

Entry: sd.delta.VM2.vect
Aliases: sd.delta.VM2.vect
Keywords: internal
Description: Standard deviation of the test statistic in the variance mixture model
URL: ../../../library/varmixt/html/sd.delta.VM2.vect.html

Entry: sd.delta.anova.vect
Aliases: sd.delta.anova.vect
Keywords: internal
Description: Vector of standard deviations of the the test statistic in homoscedastic model
URL: ../../../library/varmixt/html/sd.delta.anova.vect.html

Entry: sd.delta.gene.vect
Aliases: sd.delta.gene.vect
Keywords: internal
Description: Vector of standard deviations of the the test statistic in gene-specific model
URL: ../../../library/varmixt/html/sd.delta.gene.vect.html

Entry: sd.g.VM2.vect
Aliases: sd.g.VM2.vect
Keywords: internal
Description: Gene variance in variance mixture model
URL: ../../../library/varmixt/html/sd.g.VM2.vect.html

Entry: sd.param
Aliases: sd.param
Keywords: htest
Description: Standard deviation of the variance mixture model parameters
URL: ../../../library/varmixt/html/sd.param.html

Entry: sigma.delta.gene.vect
Aliases: sigma.delta.gene.vect
Keywords: internal
Description: Vector of standard deviations of the the test statistic in gene-specific model
URL: ../../../library/varmixt/html/sigma.delta.gene.vect.html

Entry: sigmaV2.vect
Aliases: sigmaV2.vect
Keywords: internal
Description: Vector the gene variance estimated with variance mixture model
URL: ../../../library/varmixt/html/sigmaV2.vect.html

Entry: spleen.data.vm
Aliases: spleen.data.vm
Keywords: datasets
Description: Spleen Data set
URL: ../../../library/varmixt/html/spleen.data.vm.html

Entry: stat1.data.frame
Aliases: stat1.data.frame
Keywords: internal
Description: Dataframe with simple statistics
URL: ../../../library/varmixt/html/stat1.data.frame.html

Entry: stat2.data.frame
Aliases: stat2.data.frame
Keywords: internal
Description: Data.frame with variance mixture model results
URL: ../../../library/varmixt/html/stat2.data.frame.html

Entry: test.stat.VM.vect
Aliases: test.stat.VM.vect
Keywords: internal
Description: Continuous Variance Mixture Model test statistic
URL: ../../../library/varmixt/html/test.stat.VM.vect.html

Entry: test.stat.VM2.vect
Aliases: test.stat.VM2.vect
Keywords: internal
Description: Vector of test statisitic from the variance mixture model
URL: ../../../library/varmixt/html/test.stat.VM2.vect.html

Entry: test.stat.anova.vect
Aliases: test.stat.anova.vect
Keywords: internal
Description: Vector of test statistic from the homoscedastic variance model
URL: ../../../library/varmixt/html/test.stat.anova.vect.html

Entry: test.stat.gene.vect
Aliases: test.stat.gene.vect
Keywords: internal
Description: Vector of test statistic from the gene-specific variance model
URL: ../../../library/varmixt/html/test.stat.gene.vect.html

Entry: var.estim.mat
Aliases: var.estim.mat
Keywords: internal
Description: Covariance matrix of parameters estimates
URL: ../../../library/varmixt/html/var.estim.mat.html

Entry: var.gene.vect
Aliases: var.gene.vect
Keywords: internal
Description: Gene variance vector
URL: ../../../library/varmixt/html/var.gene.vect.html

Entry: var.to.vardelta.vect
Aliases: var.to.vardelta.vect
Keywords: internal
Description: Gene log-intensity variance to mean difference variance
URL: ../../../library/varmixt/html/var.to.vardelta.vect.html

Entry: varmat
Aliases: varmat
Keywords: internal
Description: Variance matrix of the parameters estimates
URL: ../../../library/varmixt/html/varmat.html

Entry: varmixt.an
Aliases: varmixt.an
Keywords: internal
Description: Mixture model on the variance
URL: ../../../library/varmixt/html/varmixt.an.html

Entry: vm.analysis
Aliases: vm.analysis
Keywords: htest
Description: Variance mixture analysis on unpaired data
URL: ../../../library/varmixt/html/vm.analysis.html

Entry: vm.analysis.paired
Aliases: vm.analysis.paired
Keywords: htest
Description: Variance mixture analysis on paired data
URL: ../../../library/varmixt/html/vm.analysis.paired.html

Entry: vm.analysis.paired.step.1
Aliases: vm.analysis.paired.step.1
Keywords: internal
Description: First step of analysis in paired data case
URL: ../../../library/varmixt/html/vm.analysis.paired.step.1.html

Entry: vm.analysis.step.2
Aliases: vm.analysis.step.2
Keywords: internal
Description: Mixture model analysis
URL: ../../../library/varmixt/html/vm.analysis.step.2.html

Entry: vm.analysis.unpaired.step.1
Aliases: vm.analysis.unpaired.step.1
Keywords: internal
Description: First step of analysis in unpaired data case
URL: ../../../library/varmixt/html/vm.analysis.unpaired.step.1.html
