Light-weight methods for normalization and visualization of microarray data using only basic R data types

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Documentation for package `aroma.light' version 1.4.0

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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
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