RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

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Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. "Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays", TCBB/IEEE, 2011. http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38

Author
Leo Lahti <leo.lahti@iki.fi>
Date of publication
None
Maintainer
Leo Lahti <leo.lahti@iki.fi>
License
BSD_2_clause + file LICENSE
Version
1.30.0
URLs

View on Bioconductor

Man pages

calculate.rpa
RPA with HITChip
collect.hyperparameters
collect.hyperparameters
d.update.fast
Fast d update
estimate.affinities
estimate.affinities
estimate.hyperparameters
estimate.hyperparameters
frpa
frpa
get.batches
get.batches Split data into batches
get.probe.matrix
get.probe.matrix
get.probe.parameters
get.probe.parameters
get.probeset
Get probeset
hyperparameter.update
hyperparameter.update
levelmap
Map taxonomic levels
n.phylotypes.per.oligo
n.phylotypes.per.oligo
online.quantile
online.quantile Quantile normalization tools for online...
probe.parameters.tolist
probe.parameters.tolist
probe.performance
Probe performance
probeplot
probeplot Plot RPA results and probe-level data for a...
probetable
probetable
retrieve.probesets
Retrieve probesets
rpa
rpa
rpa.complete
Complete RPA preprocessing
rpa.fit
RPA fit
RPA.iteration
RPA iteration
rpa.online
rpa.online
RPA-package
RPA: probabilistic analysis of probe reliability and gene...
rpaplot
rpaplot Plot RPA results and probe-level data for a specified...
rpa.plot
rpa.plot
RPA.preprocess
RPA preprocessing
rpa.summarize
rpa.summarize
sample.probeset
sample.probeset
summarize.batch
summarize.batch
summarize.batches
summarize.batches
summarize_probedata
Summarize probedata
summarize.rpa
RPA summarization
summarize.sum
Sum-based probe summarization
updating.hyperparameters
updating hyperparameters

Files in this package

RPA/DESCRIPTION
RPA/LICENSE
RPA/NAMESPACE
RPA/R
RPA/R/AllClasses.R
RPA/R/AllGenerics.R
RPA/R/RPA-package.R
RPA/R/RPA.dcost.R
RPA/R/RPA.iteration.R
RPA/R/RPA.preprocess.R
RPA/R/RPA.tau2.update.R
RPA/R/calculate.rpa.hitchip.R
RPA/R/d.update.fast.R
RPA/R/estimate.affinities.R
RPA/R/estimate.hyperparameters.R
RPA/R/firstlib.R
RPA/R/frpa.R
RPA/R/get.probe.matrix.R
RPA/R/get.probeset.hitchip.R
RPA/R/initialize.priors.R
RPA/R/internals.R
RPA/R/levelmap.R
RPA/R/n.phylotypes.per.oligo.R
RPA/R/online.quantile.R
RPA/R/plot-methods.R
RPA/R/probe.performance.R
RPA/R/retrieve.probesets.hitchip.R
RPA/R/rpa.R
RPA/R/rpa.complete.R
RPA/R/rpa.fit.R
RPA/R/rpa.online.R
RPA/R/rpa.plot.R
RPA/R/rpa.summarize.R
RPA/R/show-methods.R
RPA/R/summarize.batch.R
RPA/R/summarize.batches.R
RPA/R/summarize.rpa.hitchip.R
RPA/R/summarize.sum.hitchip.R
RPA/R/summarize_probedata_hitchip.R
RPA/R/toydata.R
RPA/R/update.hyperparameters.R
RPA/R/updating.hyperparameters.R
RPA/README.md
RPA/inst
RPA/inst/CITATION
RPA/inst/NEWS
RPA/inst/doc
RPA/man
RPA/man/RPA-package.Rd
RPA/man/RPA.iteration.Rd
RPA/man/RPA.preprocess.Rd
RPA/man/calculate.rpa.Rd
RPA/man/collect.hyperparameters.Rd
RPA/man/d.update.fast.Rd
RPA/man/estimate.affinities.Rd
RPA/man/estimate.hyperparameters.Rd
RPA/man/frpa.Rd
RPA/man/get.batches.Rd
RPA/man/get.probe.matrix.Rd
RPA/man/get.probe.parameters.Rd
RPA/man/get.probeset.Rd
RPA/man/hyperparameter.update.Rd
RPA/man/levelmap.Rd
RPA/man/n.phylotypes.per.oligo.Rd
RPA/man/online.quantile.Rd
RPA/man/probe.parameters.tolist.Rd
RPA/man/probe.performance.Rd
RPA/man/probeplot.Rd
RPA/man/probetable.Rd
RPA/man/retrieve.probesets.Rd
RPA/man/rpa.Rd
RPA/man/rpa.complete.Rd
RPA/man/rpa.fit.Rd
RPA/man/rpa.online.Rd
RPA/man/rpa.plot.Rd
RPA/man/rpa.summarize.Rd
RPA/man/rpaplot.Rd
RPA/man/sample.probeset.Rd
RPA/man/summarize.batch.Rd
RPA/man/summarize.batches.Rd
RPA/man/summarize.rpa.Rd
RPA/man/summarize.sum.Rd
RPA/man/summarize_probedata.Rd
RPA/man/updating.hyperparameters.Rd
RPA/tests
RPA/tests/rpa.R
RPA/vignettes
RPA/vignettes/RPA.Rmd
RPA/vignettes/RPA.md