aroma.light-package | Package aroma.light |
1. Calibration and Normalization | 1. Calibration and Normalization |
aroma.light | Package aroma.light |
averageQuantile.list | Gets the average empirical distribution |
backtransformAffine.matrix | Reverse affine transformation |
calibrateMultiscan.matrix | Weighted affine calibration of a multiple re-scanned channel |
distanceBetweenLines | Finds the shortest distance between two lines |
fitIWPCA.matrix | Robust fit of linear subspace through multidimensional data |
iwpca.matrix | Fits an R-dimensional hyperplane using iterative re-weighted PCA |
likelihood.smooth.spline | Calculate the log likelihood of a smoothing spline given the data |
medianPolish.matrix | Median polish |
normalizeAffine.matrix | Weighted affine normalization between channels and arrays |
normalizeAverage.list | Rescales channel vectors to get the same average |
normalizeAverage.matrix | Rescales channel vectors to get the same average |
normalizeCurveFit.matrix | Weighted curve-fit normalization between a pair of channels |
normalizeLoess.matrix | Weighted curve-fit normalization between a pair of channels |
normalizeLowess.matrix | Weighted curve-fit normalization between a pair of channels |
normalizeQuantile.list | Normalizes the empirical distribution of a set of samples to a target distribution |
normalizeQuantile.matrix | Weighted sample quantile normalization |
normalizeQuantile.numeric | Normalizes the empirical distribution of a single sample to a target distribution |
normalizeRobustSpline.matrix | Weighted curve-fit normalization between a pair of channels |
normalizeSpline.matrix | Weighted curve-fit normalization between a pair of channels |
plotDensity.data.frame | Plots density distributions for a set of vector |
plotDensity.list | Plots density distributions for a set of vector |
plotDensity.matrix | Plots density distributions for a set of vector |
plotDensity.numeric | Plots density distributions for a set of vector |
plotMvsA.matrix | Plot log-ratios vs log-intensities |
plotMvsAPairs.matrix | Plot log-ratios/log-intensities for all unique pairs of data vectors |
plotMvsMPairs.matrix | Plot log-ratios vs log-ratios for all pairs of columns |
robustSmoothSpline | Robust fit of a Smoothing Spline |
sampleCorrelations.matrix | Calculates the correlation for random pairs of observations |
sampleTuples | Sample tuples of elements from a set |
weightedMedian | Weighted Median Value |
wpca.matrix | Light-weight Weighted Principal Component Analysis |