Removal of unwanted variation for gene-gene correlations and related analysis

assessQuality | Quality assessment for cleaning procedures. |

background | Randomly choose background genes. |

calculateThreshold | Calculates the correlation threshold. |

compareRanks | Compare ranking of known reference gene pairs. |

correlationPlot | Correlation plot to compare estimated correlations with true... |

ECDFPlot | Plot empirical cumulative distribution function for... |

eigenvaluePlot | Plot eigenvalues of SVD of the negtaive controls. |

empNegativeControls | Empirically choose negative control genes. |

findIQR | Find the inter quantile range. |

findMinmaxSamples | Find minimum and maximum samples in gene expression data. |

findWeights | Finds weights of each level of a factor. |

funcPara | Function to optimize parameters in parallel. |

funcThresh | Function to calculate correlation threshold in parallel. |

genePlot | Plot of means and inter-quantile ranges of all genes. |

histogramPlot | Plot histogram of correlations. |

is.optimizeParameters | Checking 'optimizeParameters' class. |

is.simulateGEdata | Checking 'simulateGEdata' class. |

is.Threshold | Checking 'Threshold' class. |

is.Weights | Checking 'Weights' class. |

makePosSemiDef | Makes square matrices positive semi-definite. |

makeRankedList | Make ranked list of correlations. |

mashUp | Joining two correlation matrices by diagonal. |

optimizeParameters | Optimize parameters of removal of unwanted variation. |

PCAPlot | Plot principle component analysis for gene expression data. |

plotDesign | Plot nested design structure. |

plot.optimizeParameters | Plots an object of class 'optimizeParameters'. |

plotThreshold | Plots an object of class 'Threshold'. |

print.simulateGEdata | Print an object of class 'simualteGEdata'. |

prioritise | Prioritising candidate genes. |

RLEPlot | Plots different versions of relative log expression plots |

RUVcorr | Removal of unwanted variation for gene-gene correlations. |

RUVNaiveRidge | Removal of unwanted variation for gene correlations. |

simulateGEdata | Simulate gene expression data. |

splitByFactor | Splitting a data set by a particular factor. |

wcor | Calculate weighted correlations. |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.