Propagating Uncertainty in Microarray Analysis


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Documentation for package `puma' version 1.2.0

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puma-package puma - Propagating Uncertainty in Microarray Analysis
bcomb Combining replicates for each condition
calculateLimma Calculate differential expression between conditions using limma
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
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
erfc The complementary error function
exampleE The example data of the mean gene expression levels
exampleStd The example data of the standard deviation for gene expression levels
exprReslt-class Class exprReslt
hgu95aphis Estimated parameters of the distribution of phi
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
legend2 A legend which allows longer lines
license.puma Print puma license
matrixDistance Calculate distance between two matrices
mgmos modified gamma Model for Oligonucleotide Signal
mmgmos Multi-chip modified gamma Model for Oligonucleotide Signal
newtonStep PUMA Principal Components Analysis
normalisation.gs Global scaling normalisation
numOfFactorsToUse Determine number of factors to use from an ExpressionSet
orig_pplr Probability of positive log-ratio
plot Class pumaPCARes
plot,pumaPCARes,missing-method Plot method for pumaPCARes objects
plot,pumaPCARes-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
pplr Probability of positive log-ratio
pplrUnsorted Return an unsorted matrix of PPLR values
prcfifty Class exprReslt
prcfifty,exprReslt-method Class exprReslt
prcfifty<-,exprReslt-method Class exprReslt
prcfive Class exprReslt
prcfive,exprReslt-method Class exprReslt
prcfive<-,exprReslt-method Class exprReslt
prcninfive Class exprReslt
prcninfive,exprReslt-method Class exprReslt
prcninfive<-,exprReslt-method Class exprReslt
prcsevfive Class exprReslt
prcsevfive,exprReslt-method Class exprReslt
prcsevfive<-,exprReslt-method Class exprReslt
prctwfive Class exprReslt
prctwfive,exprReslt-method Class exprReslt
prctwfive<-,exprReslt-method Class exprReslt
puma puma - Propagating Uncertainty in Microarray Analysis
pumaClust Propagate probe-level uncertainty in model-based clustering on gene expression data
pumaComb Combining replicates for each condition
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
se.exprs Class exprReslt
se.exprs,exprReslt-method Class exprReslt
se.exprs<-,exprReslt-method Class exprReslt
show,exprReslt-method Class exprReslt
write.reslts Class exprReslt
write.reslts,exprReslt-method Class exprReslt