quantro: A test for when to use quantile normalization

A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("quantro")
AuthorStephanie Hicks and Rafael Irizarry
Bioconductor views Microarray MultipleComparison Normalization Preprocessing Sequencing
Date of publicationNone
MaintainerStephanie Hicks <shicks@jimmy.harvard.edu>
LicenseGPL (>=3)
Version1.8.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/flowSorted.R R/methods.R R/plots.R
README.md
build
build/vignette.rds
data
data/datalist
data/flowSorted.RData
figure
figure/plot-distributions-boxplot.pdf
figure/plot-distributions-density.pdf
figure/quantro-plot.pdf
inst
inst/NEWS
inst/doc
inst/doc/quantro-vignette.R
inst/doc/quantro-vignette.Rnw
inst/doc/quantro-vignette.pdf
inst/objectCreation.R
inst/unitTests
inst/unitTests/test_quantro.R
man
man/MSbetween.Rd man/MSwithin.Rd man/anova.Rd man/flowSorted.Rd man/matboxplot.Rd man/matdensity.Rd man/quantro-class.Rd man/quantro.Rd man/quantroPlot.Rd man/quantroPvalPerm.Rd man/quantroStat.Rd man/quantroStatPerm.Rd man/summary.Rd
tests
tests/runTests.R
vignettes
vignettes/figure
vignettes/figure/plot-distributions-boxplot-1.pdf
vignettes/figure/plot-distributions-density-1.pdf
vignettes/figure/quantro-plot-1.pdf
vignettes/library.bib
vignettes/quantro-vignette-concordance.tex
vignettes/quantro-vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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