Entry: Clust.exampleE
Aliases: Clust.exampleE
Keywords: datasets
Description: The example data of the mean gene expression levels
URL: ../../../library/puma/html/Clust.exampleE.html

Entry: Clust.exampleStd
Aliases: Clust.exampleStd
Keywords: datasets
Description: The example data of the standard deviation for gene expression levels
URL: ../../../library/puma/html/Clust.exampleStd.html

Entry: DEResult
Aliases: class:DEResult DEResult DEResult-class statistic statistic<- FC FC<- statisticDescription statisticDescription<- DEMethod DEMethod<- pLikeValues topGenes topGeneIDs numberOfProbesets numberOfGenes numberOfContrasts statistic,DEResult-method statistic<-,DEResult,data.frame-method FC,DEResult-method FC<-,DEResult,data.frame-method statisticDescription,DEResult-method statisticDescription<-,DEResult,character-method DEMethod,DEResult-method DEMethod<-,DEResult,character-method pLikeValues,DEResult-method topGenes,DEResult-method topGeneIDs,DEResult-method numberOfProbesets,DEResult-method numberOfGenes,DEResult-method numberOfContrasts,DEResult-method show,DEResult-method write.reslts,DEResult-method
Keywords: classes
Description: Class DEResult
URL: ../../../library/puma/html/DEResult-class.html

Entry: bcomb
Aliases: bcomb
Keywords: manip models
Description: Combining replicates for each condition
URL: ../../../library/puma/html/bcomb.html

Entry: calcAUC
Aliases: calcAUC
Keywords: manip
Description: Calculate Area Under Curve (AUC) for a standard ROC plot.
URL: ../../../library/puma/html/calcAUC.html

Entry: calculateFC
Aliases: calculateFC
Keywords: manip
Description: Calculate differential expression between conditions using FC
URL: ../../../library/puma/html/calculateFC.html

Entry: calculateLimma
Aliases: calculateLimma
Keywords: manip
Description: Calculate differential expression between conditions using limma
URL: ../../../library/puma/html/calculateLimma.html

Entry: calculateTtest
Aliases: calculateTtest
Keywords: manip
Description: Calculate differential expression between conditions using T-test
URL: ../../../library/puma/html/calculateTtest.html

Entry: clusterApplyLBDots
Aliases: clusterApplyLBDots
Keywords: manip
Description: clusterApplyLB with dots to indicate progress
URL: ../../../library/puma/html/clusterApplyLBDots.html

Entry: clusterNormE
Aliases: clusterNormE
Keywords: manip
Description: Zero-centered normalisation
URL: ../../../library/puma/html/clusterNormE.html

Entry: clusterNormVar
Aliases: clusterNormVar
Keywords: manip
Description: Adjusting expression variance for zero-centered normalisation
URL: ../../../library/puma/html/clusterNormVar.html

Entry: compareLimmapumaDE
Aliases: compareLimmapumaDE
Keywords: manip
Description: Compare pumaDE with a default Limma model
URL: ../../../library/puma/html/compareLimmapumaDE.html

Entry: createContrastMatrix
Aliases: createContrastMatrix
Keywords: manip
Description: Automatically create a contrast matrix from an ExpressionSet and optional design matrix
URL: ../../../library/puma/html/createContrastMatrix.html

Entry: createDesignMatrix
Aliases: createDesignMatrix
Keywords: manip
Description: Automatically create a design matrix from an ExpressionSet
URL: ../../../library/puma/html/createDesignMatrix.html

Entry: create_eset_r
Aliases: create_eset_r
Keywords: manip
Description: Create an ExpressionSet from a PPLR matrix
URL: ../../../library/puma/html/create_eset_r.html

Entry: erfc
Aliases: erfc
Keywords: math
Description: The complementary error function
URL: ../../../library/puma/html/erfc.html

Entry: exampleE
Aliases: exampleE
Keywords: datasets
Description: The example data of the mean gene expression levels
URL: ../../../library/puma/html/exampleE.html

Entry: exampleStd
Aliases: exampleStd
Keywords: datasets
Description: The example data of the standard deviation for gene expression levels
URL: ../../../library/puma/html/exampleStd.html

Entry: exprReslt-class
Aliases: class:exprReslt exprReslt exprReslt-class se.exprs se.exprs<- prcfifty prcfifty<- prcfive prcfive<- prcninfive prcninfive<- prcsevfive prcsevfive<- prctwfive prctwfive<- write.reslts show,exprReslt-method se.exprs,exprReslt-method se.exprs<-,exprReslt-method prcfifty,exprReslt-method prcfifty<-,exprReslt-method prcfive,exprReslt-method prcfive<-,exprReslt-method prcninfive,exprReslt-method prcninfive<-,exprReslt-method prcsevfive,exprReslt-method prcsevfive<-,exprReslt-method prctwfive,exprReslt-method prctwfive<-,exprReslt-method write.reslts,exprReslt-method
Keywords: classes
Description: Class exprReslt
URL: ../../../library/puma/html/exprReslt-class.html

Entry: hgu95aphis
Aliases: hgu95aphis
Keywords: datasets
Description: Estimated parameters of the distribution of phi
URL: ../../../library/puma/html/hgu95aphis.html

Entry: justmgMOS
Aliases: justmgMOS just.mgmos
Keywords: manip
Description: Compute mgmos Directly from CEL Files
URL: ../../../library/puma/html/justmgMOS.html

Entry: justmmgMOS
Aliases: justmmgMOS just.mmgmos
Keywords: manip
Description: Compute mmgmos Directly from CEL Files
URL: ../../../library/puma/html/justmmgMOS.html

Entry: legend2
Aliases: legend2
Keywords: aplot
Description: A legend which allows longer lines
URL: ../../../library/puma/html/legend2.html

Entry: license.puma
Aliases: license.puma
Keywords: misc
Description: Print puma license
URL: ../../../library/puma/html/license.puma.html

Entry: matrixDistance
Aliases: matrixDistance
Keywords: manip
Description: Calculate distance between two matrices
URL: ../../../library/puma/html/matrixDistance.html

Entry: mgmos
Aliases: mgmos
Keywords: manip
Description: modified gamma Model for Oligonucleotide Signal
URL: ../../../library/puma/html/mgmos.html

Entry: mmgmos
Aliases: mmgmos
Keywords: manip
Description: Multi-chip modified gamma Model for Oligonucleotide Signal
URL: ../../../library/puma/html/mmgmos.html

Entry: normalisation.gs
Aliases: normalisation.gs
Keywords: manip
Description: Global scaling normalisation
URL: ../../../library/puma/html/normalisation.gs.html

Entry: numFP
Aliases: numFP
Keywords: manip
Description: Number of False Positives for a given proportion of True Positives.
URL: ../../../library/puma/html/numFP.html

Entry: numOfFactorsToUse
Aliases: numOfFactorsToUse
Keywords: manip
Description: Determine number of factors to use from an ExpressionSet
URL: ../../../library/puma/html/numOfFactorsToUse.html

Entry: numTP
Aliases: numTP
Keywords: manip
Description: Number of True Positives for a given proportion of False Positives.
URL: ../../../library/puma/html/numTP.html

Entry: orig_pplr
Aliases: orig_pplr
Keywords: manip models
Description: Probability of positive log-ratio
URL: ../../../library/puma/html/orig_pplr.html

Entry: plot-methods
Aliases: plot.pumaPCARes plot-methods plot,pumaPCARes-method plot,pumaPCARes,missing-method
Keywords: methods hplot
Description: Plot method for pumaPCARes objects
URL: ../../../library/puma/html/plot-methods.html

Entry: plotErrorBars
Aliases: plotErrorBars
Keywords: hplot
Description: Plot mean expression levels and error bars for one or more probesets
URL: ../../../library/puma/html/plotErrorBars.html

Entry: plotHistTwoClasses
Aliases: plotHistTwoClasses
Keywords: hplot
Description: Stacked histogram plot of two different classes
URL: ../../../library/puma/html/plotHistTwoClasses.html

Entry: plotROC
Aliases: plotROC
Keywords: hplot
Description: Receiver Operator Characteristic (ROC) plot
URL: ../../../library/puma/html/plotROC.html

Entry: plotWhiskers
Aliases: plotWhiskers
Keywords: hplot
Description: Standard errors whiskers plot
URL: ../../../library/puma/html/plotWhiskers.html

Entry: pplr
Aliases: pplr
Keywords: manip models
Description: Probability of positive log-ratio
URL: ../../../library/puma/html/pplr.html

Entry: pplrUnsorted
Aliases: pplrUnsorted
Keywords: manip
Description: Return an unsorted matrix of PPLR values
URL: ../../../library/puma/html/pplrUnsorted.html

Entry: puma-package
Aliases: puma-package puma
Keywords: package
Description: puma - Propagating Uncertainty in Microarray Analysis
URL: ../../../library/puma/html/puma-package.html

Entry: pumaComb
Aliases: pumaComb
Keywords: manip models
Description: Combining replicates for each condition
URL: ../../../library/puma/html/pumaComb.html

Entry: pumaDE
Aliases: pumaDE
Keywords: manip
Description: Calculate differential expression between conditions
URL: ../../../library/puma/html/pumaDE.html

Entry: pumaDEUnsorted
Aliases: pumaDEUnsorted
Keywords: manip
Description: Return an unsorted matrix of PPLR values
URL: ../../../library/puma/html/pumaDEUnsorted.html

Entry: pumaFull
Aliases: pumaFull
Keywords: manip
Description: Perform a full PUMA analysis
URL: ../../../library/puma/html/pumaFull.html

Entry: pumaNormalize
Aliases: pumaNormalize
Keywords: manip
Description: Normalize an ExpressionSet
URL: ../../../library/puma/html/pumaNormalize.html

Entry: pumaPCA
Aliases: pumaPCA pumaPCAEstep pumaPCALikelihoodBound pumaPCALikelihoodCheck pumaPCANewtonUpdateLogSigma newtonStep pumaPCARemoveRedundancy pumaPCASigmaGradient pumaPCASigmaObjective pumaPCAUpdateCinv pumaPCAUpdateM pumaPCAUpdateMu pumaPCAUpdateW
Keywords: multivariate
Description: PUMA Principal Components Analysis
URL: ../../../library/puma/html/pumaPCA.html

Entry: pumaPCAExpectations-class
Aliases: pumaPCAExpectations-class pumaPCAExpectations
Keywords: classes
Description: Class pumaPCAExpectations
URL: ../../../library/puma/html/pumaPCAExpectations-class.html

Entry: pumaPCAModel-class
Aliases: pumaPCAModel-class pumaPCAModel
Keywords: classes
Description: Class pumaPCAModel
URL: ../../../library/puma/html/pumaPCAModel-class.html

Entry: pumaPCARes-class
Aliases: pumaPCARes-class pumaPCARes plot, pumaPCARes-method
Keywords: classes
Description: Class pumaPCARes
URL: ../../../library/puma/html/pumaPCARes-class.html

Entry: pumaClust
Aliases: pumaClust
Keywords: manip models
Description: Propagate probe-level uncertainty in model-based clustering on gene expression data
URL: ../../../library/puma/html/pumaclust.html

Entry: removeUninformativeFactors
Aliases: removeUninformativeFactors
Keywords: manip
Description: Remove uninformative factors from the phenotype data of an ExpressionSet
URL: ../../../library/puma/html/removeUninformativeFactors.html
