doRMA: Robust Multichip Analysis (RMA)

Description

Robust Multichip Analysis (RMA) 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 fitPLM (package affyPLM) with great precision.

Usage

# S3 method for AffymetrixCelSet
doRMA(csR, arrays=NULL, flavor=c("affyPLM", "oligo"), uniquePlm=FALSE, drop=TRUE,
  verbose=FALSE, ...)
  # S3 method for default
doRMA(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.
flavor: A character string specifying what model fitting algorithm to be used, cf. RmaPlm.
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] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.