Entry: 1. Calibration and Normalization
Aliases: 1. Calibration and Normalization
Keywords: documentation
Description: 1. Calibration and Normalization
URL: ../../../library/aroma.light/html/1._Calibration_and_Normalization.html

Entry: Non-documented objects
Aliases: Non-documented objects fitIWPCA calibrateMultiscan normalizeAffine backtransformAffine normalizeQuantile normalizeCurveFit normalizeLoess normalizeLowess normalizeRobustSpline normalizeSpline averageQuantile plotMvsA plotMvsAPairs plotMvsMPairs plotDensity rowAverages rowAverages.matrix sampleCorrelations medianPolish projectUontoV scalarProduct tr iwpca wpca likelihood
Keywords: documentation internal
Description: Non-documented objects
URL: ../../../library/aroma.light/html/Non-documented_objects.html

Entry: aroma.light-package
Aliases: aroma.light-package aroma.light
Keywords: package
Description: Package aroma.light
URL: ../../../library/aroma.light/html/aroma.light-package.html

Entry: averageQuantile.list
Aliases: averageQuantile.list averageQuantile.list
Keywords: methods nonparametric multivariate robust
Description: Gets the average empirical distribution
URL: ../../../library/aroma.light/html/averageQuantile.list.html

Entry: backtransformAffine.matrix
Aliases: backtransformAffine.matrix backtransformAffine.matrix
Keywords: methods
Description: Reverse affine transformation
URL: ../../../library/aroma.light/html/backtransformAffine.matrix.html

Entry: calibrateMultiscan.matrix
Aliases: calibrateMultiscan.matrix calibrateMultiscan.matrix
Keywords: methods
Description: Weighted affine calibration of a multiple re-scanned channel
URL: ../../../library/aroma.light/html/calibrateMultiscan.matrix.html

Entry: distanceBetweenLines
Aliases: distanceBetweenLines.default distanceBetweenLines
Keywords: algebra
Description: Finds the shortest distance between two lines
URL: ../../../library/aroma.light/html/distanceBetweenLines.html

Entry: fitIWPCA.matrix
Aliases: fitIWPCA.matrix fitIWPCA.matrix
Keywords: methods algebra
Description: Robust fit of linear subspace through multidimensional data
URL: ../../../library/aroma.light/html/fitIWPCA.matrix.html

Entry: iwpca.matrix
Aliases: iwpca.matrix iwpca.matrix
Keywords: methods algebra
Description: Fits an R-dimensional hyperplane using iterative re-weighted PCA
URL: ../../../library/aroma.light/html/iwpca.matrix.html

Entry: likelihood.smooth.spline
Aliases: likelihood.smooth.spline likelihood.smooth.spline
Keywords: methods smooth
Description: Calculate the log likelihood of a smoothing spline given the data
URL: ../../../library/aroma.light/html/likelihood.smooth.spline.html

Entry: medianPolish.matrix
Aliases: medianPolish.matrix medianPolish.matrix
Keywords: methods algebra
Description: Median polish
URL: ../../../library/aroma.light/html/medianPolish.matrix.html

Entry: normalizeAffine.matrix
Aliases: normalizeAffine.matrix normalizeAffine.matrix
Keywords: methods
Description: Weighted affine normalization between channels and arrays
URL: ../../../library/aroma.light/html/normalizeAffine.matrix.html

Entry: normalizeCurveFit.matrix
Aliases: normalizeCurveFit.matrix normalizeCurveFit.matrix normalizeLoess.matrix normalizeLowess.matrix normalizeSpline.matrix normalizeRobustSpline.matrix
Keywords: methods
Description: Weighted curve-fit normalization between a pair of channels
URL: ../../../library/aroma.light/html/normalizeCurveFit.matrix.html

Entry: normalizeQuantile.list
Aliases: normalizeQuantile.list normalizeQuantile.list
Keywords: methods nonparametric multivariate robust
Description: Normalizes the empirical distribution of a set of samples to a target distribution
URL: ../../../library/aroma.light/html/normalizeQuantile.list.html

Entry: normalizeQuantile.matrix
Aliases: normalizeQuantile.matrix normalizeQuantile.matrix
Keywords: methods nonparametric multivariate robust
Description: Weighted sample quantile normalization
URL: ../../../library/aroma.light/html/normalizeQuantile.matrix.html

Entry: normalizeQuantile.numeric
Aliases: normalizeQuantile.numeric normalizeQuantile.numeric
Keywords: methods nonparametric multivariate robust
Description: Normalizes the empirical distribution of a single sample to a target distribution
URL: ../../../library/aroma.light/html/normalizeQuantile.numeric.html

Entry: plotDensity.list
Aliases: plotDensity.list plotDensity.list plotDensity.data.frame plotDensity.matrix plotDensity.numeric
Keywords: methods
Description: Plots density distributions for a set of vector
URL: ../../../library/aroma.light/html/plotDensity.list.html

Entry: plotMvsA.matrix
Aliases: plotMvsA.matrix plotMvsA.matrix
Keywords: methods
Description: Plot log-ratios vs log-intensities
URL: ../../../library/aroma.light/html/plotMvsA.matrix.html

Entry: plotMvsAPairs.matrix
Aliases: plotMvsAPairs.matrix plotMvsAPairs.matrix
Keywords: methods
Description: Plot log-ratios/log-intensities for all unique pairs of data vectors
URL: ../../../library/aroma.light/html/plotMvsAPairs.matrix.html

Entry: plotMvsMPairs.matrix
Aliases: plotMvsMPairs.matrix plotMvsMPairs.matrix
Keywords: methods
Description: Plot log-ratios vs log-ratios for all pairs of columns
URL: ../../../library/aroma.light/html/plotMvsMPairs.matrix.html

Entry: print.SmoothSplineLikelihood
Aliases: print.SmoothSplineLikelihood SmoothSplineLikelihood.print print.SmoothSplineLikelihood print,SmoothSplineLikelihood-method
Keywords: internal methods
Description: Prints an SmoothSplineLikelihood object
URL: ../../../library/aroma.light/html/print.SmoothSplineLikelihood.html

Entry: robustSmoothSpline
Aliases: robustSmoothSpline.default robustSmoothSpline
Keywords: smooth robust
Description: Robust fit of a Smoothing Spline
URL: ../../../library/aroma.light/html/robustSmoothSpline.html

Entry: sampleCorrelations.matrix
Aliases: sampleCorrelations.matrix sampleCorrelations.matrix
Keywords: methods utilities
Description: Calculates the correlation for random pairs of observations
URL: ../../../library/aroma.light/html/sampleCorrelations.matrix.html

Entry: sampleTuples
Aliases: sampleTuples.default sampleTuples
Keywords: utilities
Description: Sample tuples of elements from a set
URL: ../../../library/aroma.light/html/sampleTuples.html

Entry: weightedMedian
Aliases: weightedMedian.default weightedMedian
Keywords: univar robust
Description: Weighted Median Value
URL: ../../../library/aroma.light/html/weightedMedian.html

Entry: wpca.matrix
Aliases: wpca.matrix wpca.matrix
Keywords: methods algebra
Description: Light-weight Weighted Principal Component Analysis
URL: ../../../library/aroma.light/html/wpca.matrix.html
