Files in HenrikBengtsson/aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
.Rbuildignore
.Rinstignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/covr.yaml
.gitignore
.make/Makefile
CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
Makefile
NAMESPACE
NEWS.md
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
README.md
incl/BengtssonH_2003.bib.Rdoc
incl/BengtssonH_etal_2004.bib.Rdoc
incl/BengtssonH_etal_2008.bib.Rdoc
incl/BengtssonH_etal_2009.bib.Rdoc
incl/BengtssonHossjer_2006.bib.Rdoc
incl/BengtssonNeuvial_2010.bib.Rdoc
incl/backtransformAffine.matrix.Rex
incl/backtransformPrincipalCurve.matrix.Rex
incl/callNaiveGenotypes.Rex
incl/distanceBetweenLines.Rex
incl/findPeaksAndValleys.Rex
incl/fitPrincipalCurve.matrix.Rex
incl/fitXYCurve.matrix.Rex
incl/iwpca.matrix.Rex
incl/likelihood.smooth.spline.Rex
incl/medianPolish.matrix.Rex
incl/normalizeAffine.matrix.Rex
incl/normalizeCurveFit.matrix.Rex
incl/normalizeDifferencesToAverage.Rex
incl/normalizeFragmentLength-ex1.Rex
incl/normalizeFragmentLength-ex2.Rex
incl/normalizeQuantileRank.list.Rex
incl/normalizeQuantileRank.matrix.Rex
incl/normalizeQuantileSpline.matrix.Rex
incl/normalizeTumorBoost,flavors.Rex
incl/normalizeTumorBoost.Rex
incl/robustSmoothSpline.Rex
incl/sampleCorrelations.matrix.Rex
incl/sampleTuples.Rex
incl/wpca.matrix.Rex
incl/wpca2.matrix.Rex
inst/CITATION
inst/WORDLIST
inst/data-ex/PMT-RGData.dat
inst/data-ex/TumorBoost,fracB,exampleData.Rbin
inst/rsp/.rspPlugins
inst/rsp/AffineNormalization/AffineNormalization.html.rsp
inst/rsp/MultiscanCalibration/MultiscanCalibration.html.rsp
inst/rsp/NormalizationWithWeights/NormalizationWithWeights.html.rsp
inst/rsp/NormalizationWithWeights/TypesOfWeights.html
inst/rsp/R/weightedAffineNormalization.Rex
inst/rsp/R/weightedCurveFitNormalization.Rex
inst/rsp/README
inst/rsp/bgcorrection.html.rsp
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/simpleFooter.html.rsp
inst/rsp/src/simpleHead.html.rsp
inst/rsp/src/simpleHeader.html.rsp
inst/rsp/style.css
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/README.md
revdep/cran.md
revdep/failures.md
revdep/problems.md
revdep/run.R
revdep/run.sge
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
