# Propagating Uncertainty in Microarray Analysis

## Documentation for package ‘puma’ version 3.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

B C D E F G H J L M N O P R S T W

puma-package | puma - Propagating Uncertainty in Microarray Analysis

## -- B --

bcomb | Combining replicates for each condition

## -- C --

calcAUC | Calculate Area Under Curve (AUC) for a standard ROC plot.
calculateFC | Calculate differential expression between conditions using FC
calculateLimma | Calculate differential expression between conditions using limma
calculateTtest | Calculate differential expression between conditions using T-test
class:DEResult | Class DEResult
class:exprReslt | Class exprReslt
class:pumaPCARes | Class pumaPCARes
Clust.exampleE | The example data of the mean gene expression levels
Clust.exampleStd | The example data of the standard deviation for gene expression levels
clusterApplyLBDots | clusterApplyLB with dots to indicate progress
clusterNormE | Zero-centered normalisation
clusterNormVar | Adjusting expression variance for zero-centered normalisation
Clustii.exampleE | The example data of the mean gene expression levels
Clustii.exampleStd | The example data of the standard deviation for gene expression levels
compareLimmapumaDE | Compare pumaDE with a default Limma model
createContrastMatrix | Automatically create a contrast matrix from an ExpressionSet and optional design matrix
createDesignMatrix | Automatically create a design matrix from an ExpressionSet
create_eset_r | Create an ExpressionSet from a PPLR matrix

## -- D --

DEMethod | Class DEResult
DEMethod-method | Class DEResult
DEMethod<- | Class DEResult
DEMethod<--method | Class DEResult
DEResult | Class DEResult
DEResult-class | Class DEResult

## -- E --

erfc | The complementary error function
eset_mmgmos | An example ExpressionSet created from the Dilution data with mmgmos
exampleE | The example data of the mean gene expression levels
exampleStd | The example data of the standard deviation for gene expression levels
exprReslt | Class exprReslt
exprReslt-class | Class exprReslt

## -- F --

FC | Class DEResult
FC-method | Class DEResult
FC<- | Class DEResult
FC<--method | Class DEResult

## -- G --

gmoExon | Compute gene and transcript expression values and standard deviatons from exon CEL Files

## -- H --

hcomb | Combining replicates for each condition with the true gene expression
hgu95aphis | Estimated parameters of the distribution of phi

## -- J --

just.mgmos | Compute mgmos Directly from CEL Files
just.mmgmos | Compute mmgmos Directly from CEL Files
justmgMOS | Compute mgmos Directly from CEL Files
justmmgMOS | Compute mmgmos Directly from CEL Files

## -- L --

legend2 | A legend which allows longer lines
license.puma | Print puma license

## -- M --

matrixDistance | Calculate distance between two matrices
mgmos | modified gamma Model for Oligonucleotide Signal
mmgmos | Multi-chip modified gamma Model for Oligonucleotide Signal

## -- N --

newtonStep | PUMA Principal Components Analysis
normalisation.gs | Global scaling normalisation
numberOfContrasts | Class DEResult
numberOfContrasts-method | Class DEResult
numberOfGenes | Class DEResult
numberOfGenes-method | Class DEResult
numberOfProbesets | Class DEResult
numberOfProbesets-method | Class DEResult
numFP | Number of False Positives for a given proportion of True Positives.
numOfFactorsToUse | Determine number of factors to use from an ExpressionSet
numTP | Number of True Positives for a given proportion of False Positives.

## -- O --

orig_pplr | Probability of positive log-ratio

## -- P --

pLikeValues | Class DEResult
pLikeValues-method | Class DEResult
plot-method | Plot method for pumaPCARes objects
plot-methods | Plot method for pumaPCARes objects
plot.pumaPCARes | Plot method for pumaPCARes objects
plotErrorBars | Plot mean expression levels and error bars for one or more probesets
plotHistTwoClasses | Stacked histogram plot of two different classes
plotROC | Receiver Operator Characteristic (ROC) plot
plotWhiskers | Standard errors whiskers plot
PMmmgmos | Multi-chip modified gamma Model for Oligonucleotide Signal using only PM probe intensities
pplr | Probability of positive log-ratio
pplrUnsorted | Return an unsorted matrix of PPLR values
prcfifty | Class exprReslt
prcfifty-method | Class exprReslt
prcfifty<- | Class exprReslt
prcfifty<--method | Class exprReslt
prcfive | Class exprReslt
prcfive-method | Class exprReslt
prcfive<- | Class exprReslt
prcfive<--method | Class exprReslt
prcninfive | Class exprReslt
prcninfive-method | Class exprReslt
prcninfive<- | Class exprReslt
prcninfive<--method | Class exprReslt
prcsevfive | Class exprReslt
prcsevfive-method | Class exprReslt
prcsevfive<- | Class exprReslt
prcsevfive<--method | Class exprReslt
prctwfive | Class exprReslt
prctwfive-method | Class exprReslt
prctwfive<- | Class exprReslt
prctwfive<--method | Class exprReslt
puma | puma - Propagating Uncertainty in Microarray Analysis
pumaClust | Propagate probe-level uncertainty in model-based clustering on gene expression data
pumaClustii | Propagate probe-level uncertainty in robust t mixture clustering on replicated gene expression data
pumaComb | Combining replicates for each condition
pumaCombImproved | Combining replicates for each condition with the true gene expression
pumaDE | Calculate differential expression between conditions
pumaDEUnsorted | Return an unsorted matrix of PPLR values
pumaFull | Perform a full PUMA analysis
pumaNormalize | Normalize an ExpressionSet
pumaPCA | PUMA Principal Components Analysis
pumaPCAEstep | PUMA Principal Components Analysis
pumaPCAExpectations | Class pumaPCAExpectations
pumaPCAExpectations-class | Class pumaPCAExpectations
pumaPCALikelihoodBound | PUMA Principal Components Analysis
pumaPCALikelihoodCheck | PUMA Principal Components Analysis
pumaPCAModel | Class pumaPCAModel
pumaPCAModel-class | Class pumaPCAModel
pumaPCANewtonUpdateLogSigma | PUMA Principal Components Analysis
pumaPCARemoveRedundancy | PUMA Principal Components Analysis
pumaPCARes | Class pumaPCARes
pumaPCARes-class | Class pumaPCARes
pumaPCASigmaGradient | PUMA Principal Components Analysis
pumaPCASigmaObjective | PUMA Principal Components Analysis
pumaPCAUpdateCinv | PUMA Principal Components Analysis
pumaPCAUpdateM | PUMA Principal Components Analysis
pumaPCAUpdateMu | PUMA Principal Components Analysis
pumaPCAUpdateW | PUMA Principal Components Analysis

## -- R --

removeUninformativeFactors | Remove uninformative factors from the phenotype data of an ExpressionSet

## -- S --

se.exprs | Class exprReslt
se.exprs-method | Class exprReslt
se.exprs<- | Class exprReslt
se.exprs<--method | Class exprReslt
show-method | Class DEResult
show-method | Class exprReslt
statistic | Class DEResult
statistic-method | Class DEResult
statistic<- | Class DEResult
statistic<--method | Class DEResult
statisticDescription | Class DEResult
statisticDescription-method | Class DEResult
statisticDescription<- | Class DEResult
statisticDescription<--method | Class DEResult

## -- T --

topGeneIDs | Class DEResult
topGeneIDs-method | Class DEResult
topGenes | Class DEResult
topGenes-method | Class DEResult

## -- W --

write.reslts | Class exprReslt
write.reslts-method | Class DEResult
write.reslts-method | Class exprReslt
write.reslts-method | Class pumaPCARes