R: Robust Multichip Analysis (RMA) reproducing the affy package

justRMA {aroma.affymetrix}

R Documentation

Robust Multichip Analysis (RMA) reproducing the affy package

Description

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).

Usage

  ## S3 method for class 'AffymetrixCelSet'
justRMA(csR, flavor=c("oligo", "affyPLM"), ..., verbose=FALSE)
  ## Default S3 method:
justRMA(...)

Arguments

`csR`	An `AffymetrixCelSet`.
`flavor`	A `character` string specifying the estimators used in the RMA summarization step.
`...`	Additional arguments passed to `doRMA`() used internally.
`verbose`	See `Verbose`.

Value

Returns an annotated ExpressionSet.

Reproducibility of affy

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.

Author(s)

Henrik Bengtsson

References

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