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 |