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

Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

AuthorHenrik Bengtsson [aut, cre, cph], Pierre Neuvial [ctb]
Date of publicationNone
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseGPL (>= 2)
Version3.4.0
https://github.com/HenrikBengtsson/aroma.light, http://www.aroma-project.org

View on Bioconductor

Man pages

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

Files in this package

aroma.light/DESCRIPTION
aroma.light/NAMESPACE
aroma.light/NEWS
aroma.light/R
aroma.light/R/000.R
aroma.light/R/901.CalibrationAndNormalization.R
aroma.light/R/999.NonDocumentedObjects.R aroma.light/R/999.package.R aroma.light/R/averageQuantile.R aroma.light/R/backtransformAffine.R aroma.light/R/backtransformPrincipalCurve.R aroma.light/R/backtransformXYCurve.matrix.R aroma.light/R/calibrateMultiscan.R aroma.light/R/callNaiveGenotypes.R aroma.light/R/distanceBetweenLines.R aroma.light/R/findPeaksAndValleys.R aroma.light/R/fitIWPCA.R aroma.light/R/fitNaiveGenotypes.R aroma.light/R/fitPrincipalCurve.R aroma.light/R/fitXYCurve.R aroma.light/R/iwpca.R aroma.light/R/likelihood.smooth.spline.R aroma.light/R/linearAlgebra.R aroma.light/R/lines.XYCurveFit.R aroma.light/R/medianPolish.R aroma.light/R/normalizeAffine.R aroma.light/R/normalizeAverage.R
aroma.light/R/normalizeCurveFit.R
aroma.light/R/normalizeDifferencesToAverage.R aroma.light/R/normalizeFragmentLength.R aroma.light/R/normalizeQuantileRank.R aroma.light/R/normalizeQuantileRank.matrix.R aroma.light/R/normalizeQuantileSpline.R aroma.light/R/normalizeTumorBoost.R aroma.light/R/pairedAlleleSpecificCopyNumbers.R aroma.light/R/plotDensity.R aroma.light/R/plotMvsA.R aroma.light/R/plotMvsAPairs.R aroma.light/R/plotMvsMPairs.R aroma.light/R/plotXYCurve.R aroma.light/R/predict.lowess.R aroma.light/R/print.SmoothSplineLikelihood.R aroma.light/R/robustSmoothSpline.R aroma.light/R/rowAverages.matrix.R aroma.light/R/sampleCorrelations.matrix.R aroma.light/R/sampleTuples.R aroma.light/R/wpca.R aroma.light/R/zzz.R
aroma.light/inst
aroma.light/inst/CITATION
aroma.light/inst/data-ex
aroma.light/inst/data-ex/PMT-RGData.dat
aroma.light/inst/data-ex/TumorBoost,fracB,exampleData.Rbin
aroma.light/inst/rsp
aroma.light/inst/rsp/.rspPlugins
aroma.light/inst/rsp/AffineNormalization
aroma.light/inst/rsp/AffineNormalization/AffineNormalization.html.rsp
aroma.light/inst/rsp/MultiscanCalibration
aroma.light/inst/rsp/MultiscanCalibration/MultiscanCalibration.html.rsp
aroma.light/inst/rsp/NormalizationWithWeights
aroma.light/inst/rsp/NormalizationWithWeights/NormalizationWithWeights.html.rsp
aroma.light/inst/rsp/NormalizationWithWeights/TypesOfWeights.html
aroma.light/inst/rsp/R
aroma.light/inst/rsp/R/weightedAffineNormalization.Rex
aroma.light/inst/rsp/R/weightedCurveFitNormalization.Rex
aroma.light/inst/rsp/README
aroma.light/inst/rsp/bgcorrection.html.rsp
aroma.light/inst/rsp/figures
aroma.light/inst/rsp/figures/CalibrateMultiscan-GreenChannel-after.png
aroma.light/inst/rsp/figures/CalibrateMultiscan-GreenChannel-before.png
aroma.light/inst/rsp/figures/CalibrateMultiscan-RedChannel-after.png
aroma.light/inst/rsp/figures/CalibrateMultiscan-RedChannel-before.png
aroma.light/inst/rsp/figures/NormalizeAffine-after.png
aroma.light/inst/rsp/figures/NormalizeAffine-before.png
aroma.light/inst/rsp/figures/NormalizeAffine-nonweighted.png
aroma.light/inst/rsp/figures/NormalizeAffine-raw.png
aroma.light/inst/rsp/figures/NormalizeAffine-weighted.png
aroma.light/inst/rsp/figures/NormalizeCurveFit-nonweighted.png
aroma.light/inst/rsp/figures/NormalizeCurveFit-raw.png
aroma.light/inst/rsp/figures/NormalizeCurveFit-weighted.png
aroma.light/inst/rsp/index.html.rsp
aroma.light/inst/rsp/preprocessing.html.rsp
aroma.light/inst/rsp/references.html.rsp
aroma.light/inst/rsp/src
aroma.light/inst/rsp/src/simpleFooter.html.rsp
aroma.light/inst/rsp/src/simpleHead.html.rsp
aroma.light/inst/rsp/src/simpleHeader.html.rsp
aroma.light/inst/rsp/style.css
aroma.light/man
aroma.light/man/1._Calibration_and_Normalization.Rd aroma.light/man/Non-documented_objects.Rd aroma.light/man/aroma.light-package.Rd aroma.light/man/averageQuantile.Rd aroma.light/man/backtransformAffine.Rd aroma.light/man/backtransformPrincipalCurve.Rd aroma.light/man/calibrateMultiscan.Rd aroma.light/man/callNaiveGenotypes.Rd aroma.light/man/distanceBetweenLines.Rd aroma.light/man/findPeaksAndValleys.Rd aroma.light/man/fitIWPCA.Rd aroma.light/man/fitNaiveGenotypes.Rd aroma.light/man/fitPrincipalCurve.Rd aroma.light/man/fitXYCurve.Rd aroma.light/man/iwpca.Rd aroma.light/man/likelihood.smooth.spline.Rd aroma.light/man/medianPolish.Rd aroma.light/man/normalizeAffine.Rd aroma.light/man/normalizeAverage.Rd aroma.light/man/normalizeCurveFit.Rd aroma.light/man/normalizeDifferencesToAverage.Rd aroma.light/man/normalizeFragmentLength.Rd aroma.light/man/normalizeQuantileRank.Rd aroma.light/man/normalizeQuantileRank.matrix.Rd aroma.light/man/normalizeQuantileSpline.Rd aroma.light/man/normalizeTumorBoost.Rd aroma.light/man/pairedAlleleSpecificCopyNumbers.Rd aroma.light/man/plotDensity.Rd aroma.light/man/plotMvsA.Rd aroma.light/man/plotMvsAPairs.Rd aroma.light/man/plotMvsMPairs.Rd aroma.light/man/plotXYCurve.Rd aroma.light/man/print.SmoothSplineLikelihood.Rd aroma.light/man/robustSmoothSpline.Rd aroma.light/man/sampleCorrelations.Rd aroma.light/man/sampleTuples.Rd aroma.light/man/wpca.Rd
aroma.light/tests
aroma.light/tests/backtransformAffine.matrix.R
aroma.light/tests/backtransformPrincipalCurve.matrix.R
aroma.light/tests/callNaiveGenotypes.R
aroma.light/tests/distanceBetweenLines.R
aroma.light/tests/findPeaksAndValleys.R
aroma.light/tests/fitPrincipalCurve.matrix.R
aroma.light/tests/fitXYCurve.matrix.R
aroma.light/tests/iwpca.matrix.R
aroma.light/tests/likelihood.smooth.spline.R
aroma.light/tests/medianPolish.matrix.R
aroma.light/tests/normalizeAffine.matrix.R
aroma.light/tests/normalizeAverage.list.R
aroma.light/tests/normalizeAverage.matrix.R
aroma.light/tests/normalizeCurveFit.matrix.R
aroma.light/tests/normalizeDifferencesToAverage.R
aroma.light/tests/normalizeFragmentLength-ex1.R
aroma.light/tests/normalizeFragmentLength-ex2.R
aroma.light/tests/normalizeQuantileRank.list.R
aroma.light/tests/normalizeQuantileRank.matrix.R
aroma.light/tests/normalizeQuantileSpline.matrix.R
aroma.light/tests/normalizeTumorBoost,flavors.R
aroma.light/tests/normalizeTumorBoost.R
aroma.light/tests/robustSmoothSpline.R
aroma.light/tests/rowAverages.matrix.R
aroma.light/tests/sampleCorrelations.matrix.R
aroma.light/tests/sampleTuples.R
aroma.light/tests/wpca.matrix.R
aroma.light/tests/wpca2.matrix.R

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