RPA-package             RPA: probabilistic analysis of probe
                        reliability and gene expression
RPA.iteration           RPA.iteration Estimating model parameters d and
                        tau2.
RPA.preprocess          RPA.preprocess Preprocess AffyBatch object for
                        RPA.
collect.hyperparameters
                        collect.hyperparameters
d.update.fast           d.update.fast
estimate.affinities     estimate.affinities
estimate.hyperparameters
                        estimate.hyperparameters Hyperparameter
                        estimation
frpa                    frpa frozen-RPA preprocessing using
                        precalculated probe parameters
get.batches             get.batches Split data into batches
get.probe.matrix        get.probe.matrix
get.probe.parameters    get.probe.parameters
hyperparameter.update   hyperparameter.update Update hyperparameters
                        Update shape (alpha) and scale (beta)
                        parameters of the inverse gamma distribution.
online.quantile         online.quantile Quantile normalization tools
                        for online preprocessing. Estimate quantiles
                        for quantile normalization based on subset of
                        the data (random, or specified by the user).
probe.parameters.tolist
                        probe.parameters.tolist
probe.performance       probe.performance
probetable              probetable
rpa                     rpa Wrapper for RPA preprocessing.
rpa.complete            rpa.complete RPA preprocessing, also returns
                        probe parameters
rpa.fit                 rpa.fit
rpa.online              rpa.online RPA-online for preprocessing very
                        large expression data sets.
rpa.plot                rpa.plot Plot RPA results and probe-level data
                        for a specified probeset.
rpa.summarize           rpa.summarize
rpaplot                 rpaplot Plot RPA results and probe-level data
                        for a specified probeset.
sample.probeset         sample.probeset Toydata generator for probeset
                        data.
summarize.batch         summarize.batch
summarize.batches       summarize.batches
updating.hyperparameters
                        updating.hyperparameters Hyperparameter update
