Robust Multichip Analysis (RMA) reproducing the affy package as far as possible. The RMA method is described in [1].
The algorithm is processed in bounded memory, meaning a very large
number of arrays can be analyzed on also very limited computer systems.
The only limitation is the amount of memory required to load the final
chip-effect estimates into memory (as a ExpressionSet).
# S3 method for AffymetrixCelSet
justRMA(csR, flavor=c("oligo", "affyPLM"), ..., verbose=FALSE)
# S3 method for default
justRMA(...)Returns an annotated ExpressionSet.
An AffymetrixCelSet.
A character string specifying the estimators used in
the RMA summarization step.
Additional arguments passed to doRMA() used internally.
See Verbose.
This implementation of the RMA method reproduces justRMA
in affy package quite well. It does so by still using a
constant memory profile, i.e. it is possible to use this implementation
to run RMA on a much large data set than what is possible with
affy. At least 20-50 times more samples should be
doable, if not more.
Henrik Bengtsson
[1] Irizarry et al.
Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.
doRMA().