snm: Supervised Normalization of Microarrays
Version 1.24.0

SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Browse man pages Browse package API and functions Browse package files

AuthorBrig Mecham and John D. Storey <jstorey@princeton.edu>
Bioconductor views DifferentialExpression ExonArray GeneExpression Microarray MultiChannel MultipleComparison OneChannel Preprocessing QualityControl Transcription TwoChannel
Date of publicationNone
MaintainerJohn D. Storey <jstorey@princeton.edu>
LicenseLGPL
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("snm")

Man pages

fitted.snm: Extract fitted values from an snm object
plot.snm: Display plots for an snm object
sim.doubleChannel: Simulated data for a double channel microarray experiment.
sim.preProcessed: Simulate data from a microarray experiment without any...
sim.refDesign: Simulates data from a two-color microarray experiment using a...
sim.singleChannel: Simulate data from a single channel microarray experiment
snm: Perform a supervised normalization of microarray data
snm-internal: Internal snm functions.
summary.snm: Display summary information for an snm object

Functions

buildBasisFunction Man page Source code
buildBasisSplineMatrix Man page Source code
calcArrayEffects Man page Source code
calculate.nulls Man page Source code
checkArguments Man page
edge.fit Man page Source code
edge.glr Man page Source code
edge.qvalue Man page Source code
err.msg Man page Source code
estimateDifferentialExpression Man page
fit.fast.model Man page
fit.model Man page Source code
fitted.snm Man page Source code
getSpanningSet Man page Source code
make.ref.model.matrices Man page Source code
make.snm.obj Man page Source code
makeDataObject Man page Source code
plot.snm Man page Source code
remove.adjustment.vars Man page Source code
rm.zero.cols Man page Source code
sim.doubleChannel Man page Source code
sim.function.var Man page Source code
sim.intensity.dep Man page Source code
sim.preProcessed Man page Source code
sim.probe.specific Man page Source code
sim.refDesign Man page Source code
sim.singleChannel Man page Source code
snm Man page Source code
snm.diagnostic.plot Man page Source code
snm.fitted Man page Source code
snm.plot Man page Source code
snm.summary Man page Source code
summary.snm Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/buildBasisFunction.R
R/buildBasisSplineMatrix.R
R/calcArrayEffects.R
R/calculate.nulls.R
R/edge.fit.R
R/edge.glr.R
R/edge.qvalue.R
R/err.msg.R
R/fit.model.R
R/fitted.snm.R
R/getSpanningSet.R
R/make.ref.model.matrices.R
R/make.snm.obj.R
R/makeDataObject.R
R/plot.snm.R
R/removeAdjustmentsVars.R
R/rm.zero.cols.R
R/sim.doubleChannel.R
R/sim.function.var.R
R/sim.intensity.dep.R
R/sim.preProcessed.R
R/sim.probe.specific.R
R/sim.refDesign.R
R/sim.singleChannel.R
R/snm.R
R/snm.diagnosticPlot.R
R/summary.snm.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/snm.R
inst/doc/snm.Rnw
inst/doc/snm.pdf
man
man/fitted.snm.Rd
man/plot.snm.Rd
man/sim.doubleChannel.Rd
man/sim.preProcessed.Rd
man/sim.refDesign.Rd
man/sim.singleChannel.Rd
man/snm-internal.Rd
man/snm.Rd
man/summary.snm.Rd
vignettes
vignettes/egDiagPlot.png
vignettes/snm.Rnw
vignettes/snm.bib
snm documentation built on May 20, 2017, 10:29 p.m.