B C D E F G H I J L M N O P R S T W
puma-package | puma - Propagating Uncertainty in Microarray Analysis |
bcomb | Combining replicates for each condition |
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 |
DEMethod | Class DEResult |
DEMethod-method | Class DEResult |
DEMethod<- | Class DEResult |
DEMethod<--method | Class DEResult |
DEResult | Class DEResult |
DEResult-class | Class DEResult |
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 |
FC | Class DEResult |
FC-method | Class DEResult |
FC<- | Class DEResult |
FC<--method | Class DEResult |
gmhta | Compute gene and transcript expression values and standard deviatons from hta2.0 CEL Files |
gmoExon | Compute gene and transcript expression values and standard deviatons from exon CEL Files |
hcomb | Combining replicates for each condition with the true gene expression |
hgu95aphis | Estimated parameters of the distribution of phi |
igmoExon | Separately Compute gene and transcript expression values and standard deviatons from exon CEL Files by the conditions. |
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 |
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. |
orig_pplr | Probability of positive log-ratio |
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 |
removeUninformativeFactors | Remove uninformative factors from the phenotype data of an ExpressionSet |
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 |
topGeneIDs | Class DEResult |
topGeneIDs-method | Class DEResult |
topGenes | Class DEResult |
topGenes-method | Class DEResult |
write.reslts | Class exprReslt |
write.reslts-method | Class DEResult |
write.reslts-method | Class exprReslt |
write.reslts-method | Class pumaPCARes |