Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

1._Calibration_and_Normalization | 1. Calibration and Normalization |

aroma.light-package | Package aroma.light |

averageQuantile | Gets the average empirical distribution |

backtransformAffine | Reverse affine transformation |

backtransformPrincipalCurve | Reverse transformation of principal-curve fit |

calibrateMultiscan | Weighted affine calibration of a multiple re-scanned channel |

callNaiveGenotypes | Calls genotypes in a normal sample |

distanceBetweenLines | Finds the shortest distance between two lines |

findPeaksAndValleys | Finds extreme points in the empirical density estimated from... |

fitIWPCA | Robust fit of linear subspace through multidimensional data |

fitNaiveGenotypes | Fit naive genotype model from a normal sample |

fitPrincipalCurve | Fit a principal curve in K dimensions |

fitXYCurve | Fitting a smooth curve through paired (x,y) data |

iwpca | Fits an R-dimensional hyperplane using iterative re-weighted... |

likelihood.smooth.spline | Calculate the log likelihood of a smoothing spline given the... |

medianPolish | Median polish |

Non-documented_objects | Non-documented objects |

normalizeAffine | Weighted affine normalization between channels and arrays |

normalizeAverage | Rescales channel vectors to get the same average |

normalizeCurveFit | Weighted curve-fit normalization between a pair of channels |

normalizeDifferencesToAverage | Rescales channel vectors to get the same average |

normalizeFragmentLength | Normalizes signals for PCR fragment-length effects |

normalizeQuantileRank | Normalizes the empirical distribution of one of more samples... |

normalizeQuantileRank.matrix | Normalizes the empirical distribution of a set of samples to... |

normalizeQuantileSpline | Normalizes the empirical distribution of one or more samples... |

normalizeTumorBoost | Normalizes allele B fractions for a tumor given a match... |

pairedAlleleSpecificCopyNumbers | Calculating tumor-normal paired allele-specific copy number... |

plotDensity | Plots density distributions for a set of vectors |

plotMvsA | Plot log-ratios vs log-intensities |

plotMvsAPairs | Plot log-ratios/log-intensities for all unique pairs of data... |

plotMvsMPairs | Plot log-ratios vs log-ratios for all pairs of columns |

plotXYCurve | Plot the relationship between two variables as a smooth curve |

print.SmoothSplineLikelihood | Prints an SmoothSplineLikelihood object |

robustSmoothSpline | Robust fit of a Smoothing Spline |

sampleCorrelations | Calculates the correlation for random pairs of observations |

sampleTuples | Sample tuples of elements from a set |

wpca | Light-weight Weighted Principal Component Analysis |

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