aroma.light: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Version 3.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHenrik Bengtsson [aut, cre, cph], Pierre Neuvial [ctb]
Bioconductor views Infrastructure Microarray MultiChannel OneChannel Preprocessing TwoChannel Visualization
Date of publicationNone
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseGPL (>= 2)
Version3.6.0
URL https://github.com/HenrikBengtsson/aroma.light http://www.aroma-project.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("aroma.light")

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

Functions

1. Calibration and Normalization Man page
Non-documented objects Man page
SmoothSplineLikelihood.print Man page
aroma.light Man page
aroma.light-package Man page
averageQuantile Man page
averageQuantile.list Man page
averageQuantile.matrix Man page
backtransformAffine Man page
backtransformAffine.matrix Man page
backtransformPrincipalCurve Man page
backtransformPrincipalCurve.matrix Man page
backtransformPrincipalCurve.numeric Man page
backtransformXYCurve Man page
backtransformXYCurve.matrix Man page
calibrateMultiscan Man page
calibrateMultiscan.matrix Man page
callNaiveGenotypes Man page
callNaiveGenotypes.numeric Man page
distanceBetweenLines Man page
distanceBetweenLines.default Man page
findPeaksAndValleys Man page
findPeaksAndValleys.density Man page
findPeaksAndValleys.numeric Man page
fitIWPCA Man page
fitIWPCA.matrix Man page
fitNaiveGenotypes Man page
fitNaiveGenotypes.numeric Man page
fitPrincipalCurve Man page
fitPrincipalCurve.matrix Man page
fitXYCurve Man page
fitXYCurve.matrix Man page
iwpca Man page
iwpca.matrix Man page
likelihood Man page
likelihood.smooth.spline Man page
lines.XYCurveFit Man page
medianPolish Man page
medianPolish.matrix Man page
normalizeAffine Man page
normalizeAffine.matrix Man page
normalizeAverage Man page
normalizeAverage.list Man page
normalizeAverage.matrix Man page
normalizeCurveFit Man page
normalizeCurveFit.matrix Man page
normalizeDifferencesToAverage Man page
normalizeDifferencesToAverage.list Man page
normalizeFragmentLength Man page
normalizeFragmentLength.default Man page
normalizeLoess Man page
normalizeLoess.matrix Man page
normalizeLowess Man page
normalizeLowess.matrix Man page
normalizeQuantile Man page
normalizeQuantile.default Man page
normalizeQuantileRank Man page
normalizeQuantileRank.list Man page
normalizeQuantileRank.matrix Man page
normalizeQuantileRank.numeric Man page
normalizeQuantileSpline Man page
normalizeQuantileSpline.list Man page
normalizeQuantileSpline.matrix Man page
normalizeQuantileSpline.numeric Man page
normalizeRobustSpline Man page
normalizeRobustSpline.matrix Man page
normalizeSpline Man page
normalizeSpline.matrix Man page
normalizeTumorBoost Man page
normalizeTumorBoost.numeric Man page
onAttach Source code
onLoad Source code
pairedAlleleSpecificCopyNumbers Man page
pairedAlleleSpecificCopyNumbers.numeric Man page
plotDensity Man page
plotDensity.data.frame Man page
plotDensity.density Man page
plotDensity.list Man page
plotDensity.matrix Man page
plotDensity.numeric Man page
plotMvsA Man page
plotMvsA.matrix Man page
plotMvsAPairs Man page
plotMvsAPairs.matrix Man page
plotMvsMPairs Man page
plotMvsMPairs.matrix Man page
plotXYCurve Man page
plotXYCurve.matrix Man page
plotXYCurve.numeric Man page
predict.lowess Man page
print,SmoothSplineLikelihood-method Man page
print.SmoothSplineLikelihood Man page
projectUontoV Man page Source code
robustSmoothSpline Man page
robustSmoothSpline.default Man page
rowAverages Man page
rowAverages.matrix Man page
sampleCorrelations Man page
sampleCorrelations.matrix Man page
sampleTuples Man page
sampleTuples.default Man page
scalarProduct Man page Source code
tr Man page Source code
whichUnique Source code
wpca Man page
wpca.matrix Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/000.R
R/901.CalibrationAndNormalization.R
R/999.NonDocumentedObjects.R
R/999.package.R
R/averageQuantile.R
R/backtransformAffine.R
R/backtransformPrincipalCurve.R
R/backtransformXYCurve.matrix.R
R/calibrateMultiscan.R
R/callNaiveGenotypes.R
R/distanceBetweenLines.R
R/findPeaksAndValleys.R
R/fitIWPCA.R
R/fitNaiveGenotypes.R
R/fitPrincipalCurve.R
R/fitXYCurve.R
R/iwpca.R
R/likelihood.smooth.spline.R
R/linearAlgebra.R
R/lines.XYCurveFit.R
R/medianPolish.R
R/normalizeAffine.R
R/normalizeAverage.R
R/normalizeCurveFit.R
R/normalizeDifferencesToAverage.R
R/normalizeFragmentLength.R
R/normalizeQuantileRank.R
R/normalizeQuantileRank.matrix.R
R/normalizeQuantileSpline.R
R/normalizeTumorBoost.R
R/pairedAlleleSpecificCopyNumbers.R
R/plotDensity.R
R/plotMvsA.R
R/plotMvsAPairs.R
R/plotMvsMPairs.R
R/plotXYCurve.R
R/predict.lowess.R
R/print.SmoothSplineLikelihood.R
R/robustSmoothSpline.R
R/rowAverages.matrix.R
R/sampleCorrelations.matrix.R
R/sampleTuples.R
R/wpca.R
R/zzz.R
inst
inst/CITATION
inst/data-ex
inst/data-ex/PMT-RGData.dat
inst/data-ex/TumorBoost,fracB,exampleData.Rbin
inst/rsp
inst/rsp/.rspPlugins
inst/rsp/AffineNormalization
inst/rsp/AffineNormalization/AffineNormalization.html.rsp
inst/rsp/MultiscanCalibration
inst/rsp/MultiscanCalibration/MultiscanCalibration.html.rsp
inst/rsp/NormalizationWithWeights
inst/rsp/NormalizationWithWeights/NormalizationWithWeights.html.rsp
inst/rsp/NormalizationWithWeights/TypesOfWeights.html
inst/rsp/R
inst/rsp/R/weightedAffineNormalization.Rex
inst/rsp/R/weightedCurveFitNormalization.Rex
inst/rsp/README
inst/rsp/bgcorrection.html.rsp
inst/rsp/figures
inst/rsp/figures/CalibrateMultiscan-GreenChannel-after.png
inst/rsp/figures/CalibrateMultiscan-GreenChannel-before.png
inst/rsp/figures/CalibrateMultiscan-RedChannel-after.png
inst/rsp/figures/CalibrateMultiscan-RedChannel-before.png
inst/rsp/figures/NormalizeAffine-after.png
inst/rsp/figures/NormalizeAffine-before.png
inst/rsp/figures/NormalizeAffine-nonweighted.png
inst/rsp/figures/NormalizeAffine-raw.png
inst/rsp/figures/NormalizeAffine-weighted.png
inst/rsp/figures/NormalizeCurveFit-nonweighted.png
inst/rsp/figures/NormalizeCurveFit-raw.png
inst/rsp/figures/NormalizeCurveFit-weighted.png
inst/rsp/index.html.rsp
inst/rsp/preprocessing.html.rsp
inst/rsp/references.html.rsp
inst/rsp/src
inst/rsp/src/simpleFooter.html.rsp
inst/rsp/src/simpleHead.html.rsp
inst/rsp/src/simpleHeader.html.rsp
inst/rsp/style.css
man
man/1._Calibration_and_Normalization.Rd
man/Non-documented_objects.Rd
man/aroma.light-package.Rd
man/averageQuantile.Rd
man/backtransformAffine.Rd
man/backtransformPrincipalCurve.Rd
man/calibrateMultiscan.Rd
man/callNaiveGenotypes.Rd
man/distanceBetweenLines.Rd
man/findPeaksAndValleys.Rd
man/fitIWPCA.Rd
man/fitNaiveGenotypes.Rd
man/fitPrincipalCurve.Rd
man/fitXYCurve.Rd
man/iwpca.Rd
man/likelihood.smooth.spline.Rd
man/medianPolish.Rd
man/normalizeAffine.Rd
man/normalizeAverage.Rd
man/normalizeCurveFit.Rd
man/normalizeDifferencesToAverage.Rd
man/normalizeFragmentLength.Rd
man/normalizeQuantileRank.Rd
man/normalizeQuantileRank.matrix.Rd
man/normalizeQuantileSpline.Rd
man/normalizeTumorBoost.Rd
man/pairedAlleleSpecificCopyNumbers.Rd
man/plotDensity.Rd
man/plotMvsA.Rd
man/plotMvsAPairs.Rd
man/plotMvsMPairs.Rd
man/plotXYCurve.Rd
man/print.SmoothSplineLikelihood.Rd
man/robustSmoothSpline.Rd
man/sampleCorrelations.Rd
man/sampleTuples.Rd
man/wpca.Rd
revdep
revdep/check.R
revdep/checks.rds
revdep/problems.md
revdep/timing.md
tests
tests/backtransformAffine.matrix.R
tests/backtransformPrincipalCurve.matrix.R
tests/callNaiveGenotypes.R
tests/distanceBetweenLines.R
tests/findPeaksAndValleys.R
tests/fitPrincipalCurve.matrix.R
tests/fitXYCurve.matrix.R
tests/iwpca.matrix.R
tests/likelihood.smooth.spline.R
tests/medianPolish.matrix.R
tests/normalizeAffine.matrix.R
tests/normalizeAverage.list.R
tests/normalizeAverage.matrix.R
tests/normalizeCurveFit.matrix.R
tests/normalizeDifferencesToAverage.R
tests/normalizeFragmentLength-ex1.R
tests/normalizeFragmentLength-ex2.R
tests/normalizeQuantileRank.list.R
tests/normalizeQuantileRank.matrix.R
tests/normalizeQuantileSpline.matrix.R
tests/normalizeTumorBoost,flavors.R
tests/normalizeTumorBoost.R
tests/robustSmoothSpline.R
tests/rowAverages.matrix.R
tests/sampleCorrelations.matrix.R
tests/sampleTuples.R
tests/wpca.matrix.R
tests/wpca2.matrix.R
aroma.light documentation built on May 20, 2017, 10:51 p.m.