summarize.batches: summarize.batches
In RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

Description Usage Arguments Details Value Author(s) References Examples

Summarize batches.

summarize.batches(sets = NULL, probe.parameters = list(), batches,
  load.batches = FALSE, mc.cores = 1, cdf = NULL, bg.method = "rma",
  normalization.method = "quantiles", verbose = TRUE,
  save.batches.dir = ".", unique.run.identifier = NULL,
  save.batches = FALSE, set.inds, speedup = FALSE,
  summarize.with.affinities = FALSE)

`sets`	Probesets to summarize
`probe.parameters`	Optional probe parameters, including priors.
`batches`	Data batches for online learning
`load.batches`	Logical. Load precalculated data for the batches.
`mc.cores`	Number of cores for parallel computation
`cdf`	CDF for alternative probeset definitions
`bg.method`	Background correction method
`normalization.method`	Normalization method
`verbose`	Print progress information
`save.batches.dir`	Specify the output directory for temporary batch saves.
`unique.run.identifier`	Define identifier for this run for naming the temporary batch files. By default, a random id is generated.
`save.batches`	Save batches?
`set.inds`	Probeset indices
`speedup`	Speed up calculations with approximations.
`summarize.with.affinities`	Use affinity estimates in probe summarization step. Default: FALSE.

Sweeps through the batches. Summarizes the probesets within each batch based on the precalculated model parameter point estimates.

Expression matrix: probesets x samples.

Leo Lahti leo.lahti@iki.fi

See citation("RPA")

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Loading required package: Biobase
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RPA Copyright (C) 2008-2016 Leo Lahti.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under the FreeBSD open source license.

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