RPA (version 1.28.0)

frpa: frpa

Description

Frozen-RPA preprocessing using precalculated probe parameters.

Usage

frpa(abatch = NULL, probe.parameters = NULL, verbose = FALSE, cdf = NULL, cel.files = NULL, cel.path = NULL, mc.cores = 1, summarize.with.affinities = FALSE)

Arguments

abatch

An AffyBatch object.

probe.parameters

A list with tau2 (probe variance), quantile.basis (basis for quantile normalization in log2 domain), and optionally affinity (probe affinities). The probe.parameters$tau2 and probe.parameters$affinity are lists, each element corresponding to a probeset and containing a parameter vector over the probes. The quantile.basis is a vector over the probes, the probes need to be listed in the same order as in tau2 and affinity. probe.parameters can be optionally provided as a data frame.

verbose

Print progress information during computation.

cdf

Specify an alternative CDF environment. Default: none.

cel.files

List of CEL files to preprocess.

cel.path

Path to CEL file directory.

mc.cores

Number of cores for parallelized processing.

summarize.with.affinities

Use affinity estimates in probe summarization step. Default: FALSE.

Value

Preprocessed expression matrix in expressionSet format

Details

fRPA function to preprocess Affymetrix CEL files with RPA using precalculated (frozen) probe parameters.

References

See citation("RPA")

See Also

rpa, AffyBatch, ExpressionSet

Examples

# eset <- frpa(abatch, probe.parameters)