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 normalizeAverage backtransformAffine normalizeQuantile normalizeQuantile.default normalizeQuantileRank normalizeQuantileSpline normalizeCurveFit normalizeLoess normalizeLowess normalizeRobustSpline normalizeSpline averageQuantile plotMvsA plotMvsAPairs plotMvsMPairs plotDensity plotXYCurve rowAverages rowAverages.matrix sampleCorrelations medianPolish projectUontoV scalarProduct tr iwpca wpca fitPrincipalCurve backtransformPrincipalCurve principal.curve.hb likelihood predict.lowess
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: backtransformPrincipalCurve.matrix
Aliases: backtransformPrincipalCurve.matrix backtransformPrincipalCurve.matrix backtransformPrincipalCurve.numeric
Keywords: methods
Description: Reverse transformation of principal-curve fit
URL: ../../../library/aroma.light/html/backtransformPrincipalCurve.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: fitPrincipalCurve.matrix
Aliases: fitPrincipalCurve.matrix fitPrincipalCurve.matrix
Keywords: methods
Description: Fit a principal curve in K dimensions
URL: ../../../library/aroma.light/html/fitPrincipalCurve.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: normalizeAverage.matrix
Aliases: normalizeAverage.matrix normalizeAverage.matrix normalizeAverage.list
Keywords: methods
Description: Rescales channel vectors to get the same average
URL: ../../../library/aroma.light/html/normalizeAverage.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: normalizeFragmentLength
Aliases: normalizeFragmentLength.default normalizeFragmentLength
Keywords: nonparametric robust
Description: Normalizes signals for PCR fragment-length effects
URL: ../../../library/aroma.light/html/normalizeFragmentLength.html

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

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

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

Entry: normalizeQuantileSpline.list
Aliases: normalizeQuantileSpline.list normalizeQuantileSpline.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/normalizeQuantileSpline.list.html

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

Entry: normalizeQuantileSpline.numeric
Aliases: normalizeQuantileSpline.numeric normalizeQuantileSpline.numeric
Keywords: methods nonparametric multivariate robust
Description: Normalizes the empirical distribution of a single sample to a target distribution
URL: ../../../library/aroma.light/html/normalizeQuantileSpline.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: plotXYCurve.matrix
Aliases: plotXYCurve.matrix plotXYCurve.matrix
Keywords: methods nonparametric multivariate robust
Description: Plot the relationship between two variables as a smooth curve
URL: ../../../library/aroma.light/html/plotXYCurve.matrix.html

Entry: plotXYCurve.numeric
Aliases: plotXYCurve.numeric plotXYCurve.numeric
Keywords: methods nonparametric multivariate robust
Description: Plot the relationship between two variables as a smooth curve
URL: ../../../library/aroma.light/html/plotXYCurve.numeric.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
