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

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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.

See Also

doRMA().

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.