Man pages for puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
| 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... |
| calculateTtest | Calculate differential expression between conditions using... |
| clusterApplyLBDots | clusterApplyLB with dots to indicate progress |
| clusterNormE | Zero-centered normalisation |
| clusterNormVar | Adjusting expression variance for zero-centered normalisation |
| Clust.exampleE | The example data of the mean gene expression levels |
| Clust.exampleStd | The example data of the standard deviation for gene... |
| Clustii.exampleE | The example data of the mean gene expression levels |
| Clustii.exampleStd | The example data of the standard deviation for gene... |
| compareLimmapumaDE | Compare pumaDE with a default Limma model |
| createContrastMatrix | Automatically create a contrast matrix from an ExpressionSet... |
| createDesignMatrix | Automatically create a design matrix from an ExpressionSet |
| create_eset_r | Create an ExpressionSet from a PPLR matrix |
| DEResult-class | Class DEResult |
| erfc | The complementary error function |
| eset_mmgmos | An example ExpressionSet created from the Dilution data with... |
| exampleE | The example data of the mean gene expression levels |
| exampleStd | The example data of the standard deviation for gene... |
| exprReslt-class | Class exprReslt |
| gmhta | Compute gene and transcript expression values and standard... |
| gmoExon | Compute gene and transcript expression values and standard... |
| hcomb | Combining replicates for each condition with the true gene... |
| hgu95aphis | Estimated parameters of the distribution of phi |
| igmoExon | Separately Compute gene and transcript expression values and... |
| 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 |
| normalisation.gs | Global scaling normalisation |
| numFP | Number of False Positives for a given proportion of True... |
| numOfFactorsToUse | Determine number of factors to use from an ExpressionSet |
| numTP | Number of True Positives for a given proportion of False... |
| orig_pplr | Probability of positive log-ratio |
| plotErrorBars | Plot mean expression levels and error bars for one or more... |
| plotHistTwoClasses | Stacked histogram plot of two different classes |
| plot-methods | Plot method for pumaPCARes objects |
| plotROC | Receiver Operator Characteristic (ROC) plot |
| plotWhiskers | Standard errors whiskers plot |
| PMmmgmos | Multi-chip modified gamma Model for Oligonucleotide Signal... |
| pplr | Probability of positive log-ratio |
| pplrUnsorted | Return an unsorted matrix of PPLR values |
| pumaclust | Propagate probe-level uncertainty in model-based clustering... |
| pumaClustii | Propagate probe-level uncertainty in robust t mixture... |
| pumaComb | Combining replicates for each condition |
| pumaCombImproved | Combining replicates for each condition with the true gene... |
| pumaDE | Calculate differential expression between conditions |
| pumaDEUnsorted | Return an unsorted matrix of PPLR values |
| pumaFull | Perform a full PUMA analysis |
| pumaNormalize | Normalize an ExpressionSet |
| puma-package | puma - Propagating Uncertainty in Microarray Analysis |
| pumaPCA | PUMA Principal Components Analysis |
| pumaPCAExpectations-class | Class pumaPCAExpectations |
| pumaPCAModel-class | Class pumaPCAModel |
| pumaPCARes-class | Class pumaPCARes |
| removeUninformativeFactors | Remove uninformative factors from the phenotype data of an... |
