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aroma.affymetrix (version 2.10.0)

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 class 'AffymetrixCelSet':
doRMA(csR, arrays=NULL, flavor=c("affyPLM", "oligo"), uniquePlm=FALSE, drop=TRUE,
  verbose=FALSE, ...)
  ## S3 method for class 'default':
doRMA(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet
An AffymetrixCelSet (or the name of an AffymetrixCelSet).
arrays
A integer vector specifying the subset of arrays to run RMA on. If NULL, all arrays are considere
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 summarizati
drop
If TRUE, the RMA 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).

Value

  • Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object (containing the RMA summaries).

References

[1] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.