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... |

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