quantro: A test for when to use quantile normalization

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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.

Author
Stephanie Hicks and Rafael Irizarry
Date of publication
None
Maintainer
Stephanie Hicks <shicks@jimmy.harvard.edu>
License
GPL (>=3)
Version
1.8.0

View on Bioconductor

Man pages

anova
Accessors for the 'anova' slot of a quantro object.
flowSorted
A subset of FlowSorted.DLPFC.450k data set
matboxplot
Box plots of columns in a matrix
matdensity
Density plots of columns in a matrix
MSbetween
Accessors for the 'MSbetween' slot of a quantro object.
MSwithin
Accessors for the 'MSwithin' slot of a quantro object.
quantro
quantro
quantro-class
quantro
quantroPlot
Plot results from 'quantro' function.
quantroPvalPerm
Accessors for the 'quantroPvalPerm' slot of a quantro object.
quantroStat
Accessors for the 'quantroStat' slot of a quantro object.
quantroStatPerm
Accessors for the 'quantroStatPerm' slot of a quantro object.
summary
Accessors for the 'summary' slot of a quantro object.

Files in this package

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