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

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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.

Author
Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [ctb]
Date of publication
None
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
GPL (>= 2)
Version
3.4.0
URLs

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