doGCRMA: Robust Multichip Analysis (GCRMA)

Description

Robust Multichip Analysis (GCRMA) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems. The method replicates the results of gcrma (package gcrma) with great precision.

Usage

# S3 method for AffymetrixCelSet
doGCRMA(csR, arrays=NULL, type=c("fullmodel", "affinities"), uniquePlm=FALSE, drop=TRUE,
  verbose=FALSE, ...)
  # S3 method for default
doGCRMA(dataSet, ..., verbose=FALSE)

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Arguments

csR, dataSet: An AffymetrixCelSet (or the name of an AffymetrixCelSet).
arrays: A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.
type: A character string specifying what type of model to use for the GCRMA background correction. For more details, see GcRmaBackgroundCorrection.
uniquePlm: If TRUE, the log-additive probe-summarization model is done on probeset with unique sets of probes. If FALSE, the summarization is done on "as-is" probesets as specified by the CDF.
drop: If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.
verbose: See Verbose.
...: Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Author

Henrik Bengtsson

References

[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer. A Model Based Background Adjustment for Oligonucleotide Expression Arrays, JASA, 2004.