A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
The preferred way to install this package is:
source("https://callr.org/install#aroma.affymetrix")
To get started, see the online user guides and the vignettes https://www.aroma-project.org/.
In order to keep improving and providing support for this project, please cite references [1], [2], or any applicable publication listed on https://aroma-project.org/publications/, whenever you publish work that have been used any of the Aroma Framework.
Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial, Elizabeth Purdom, Mark Robinson, Ken Simpson
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private license (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
[1] H. Bengtsson, K. Simpson, J. Bullard, and K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008.
[2] H. Bengtsson, R. Irizarry, B. Carvalho, and T. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.
[3] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/
For a complete list, see https://aroma-project.org/publications/.