This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the diskspace that limits what number of arrays can be analyzed.

To install this package directly within R type: install.packages("aroma.affymetrix", repos="http://R-Forge.R-project.org")

Version: 1.3.3 | Last change: 2009-11-20 14:23:48+01 | Rev.: 1748

Stable Release: Get aroma.affymetrix 1.3.0 from CRAN

This package provides method for analysis of Agilent data.

To install this package directly within R type: install.packages("aroma.agilent", repos="http://R-Forge.R-project.org")

Version: 0.1.1 | Last change: 2009-11-11 18:40:48+01 | Rev.: 1727

THIS PACKAGE HAS BEEN DEPRECATED. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensites. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speed up the read substantially. This package is supporting the aroma.affymetrix package and not intended to be used elsewhere.)

To install this package directly within R type: install.packages("aroma.apd", repos="http://R-Forge.R-project.org")

Version: 0.1.7 | Last change: 2009-10-17 09:15:27+02 | Rev.: 1672

Stable Release: Get aroma.apd 0.1.7 from CRAN

This package provides R methods to interact with BioArray Software Environment (BASE). The BaseFile class provides an API for easy to loading, retrieving, modifying, and saving BASE files. The static class BasePluginDispatcher is used to call R plugins by taking care of importing data from BASE, automatic exception handling, logging to file, returning data to BASE etc.

To install this package directly within R type: install.packages("aroma.Base", repos="http://R-Forge.R-project.org")

Version: 0.4.8 | Last change: 2009-09-18 21:27:22+02 | Rev.: 1652

Package for analysis of copy-number estimates obtained from various platforms.

To install this package directly within R type: install.packages("aroma.cn", repos="http://R-Forge.R-project.org")

Version: 0.4.1 | Last change: 2009-11-13 10:29:11+01 | Rev.: 1733

This package is a private for now.

To install this package directly within R type: install.packages("aroma.cn.eval", repos="http://R-Forge.R-project.org")

Version: 0.1.1 | Last change: 2009-11-04 06:38:09+01 | Rev.: 1718

This package is a private support package for aroma.affymetrix et al. The methods and classes of this package are independent of platform. Its API is in alpha and beta stage.

To install this package directly within R type: install.packages("aroma.core", repos="http://R-Forge.R-project.org")

Version: 1.3.3 | Last change: 2009-11-22 14:58:20+01 | Rev.: 1749

Stable Release: Get aroma.core 1.3.1 from CRAN

Utility functions for accessing the public and protected data files at the The Cancer Genome Atlas (TCGA) Data Collection Center (DCC). This package is very much in an alpha stage where the API keeps changing from day to day.

To install this package directly within R type: install.packages("aroma.tcga", repos="http://R-Forge.R-project.org")

Version: 0.2.3 | Last change: 2009-11-13 17:11:48+01 | Rev.: 1734

This package provides methods for reading CFH files generated by the CNAG software.

To install this package directly within R type: install.packages("cnagIO", repos="http://R-Forge.R-project.org")

Version: 0.1.1 | Last change: 2009-09-07 00:50:50+02 | Rev.: 1627

This package provides methods for reading DCP and CDF.bin files generated by the dChip software.

To install this package directly within R type: install.packages("dChipIO", repos="http://R-Forge.R-project.org")

Version: 0.1.1 | Last change: 2009-10-03 22:11:51+02 | Rev.: 1663

DO NOT INSTALL THIS PACKAGE. THIS IS AN EMPTY PACKAGE WITH THE SAME NAME AS AN EXISTING BIOC PACKAGE. THE ONLY PURPOSE OF THIS PACKAGE IS TO PREVENT THE R-FORGE BUILD SERVERS TO HALT THE BUILDING OF AROMA.CORE AND AROMA.AFFYMETRIX. THIS DUMMY PACKAGE WILL NOT BE NEEDED WHEN R-FORGE INCLUDES THE REAL EBIMAGE PACKAGE OR SETS R_check_force_suggests=false

To install this package directly within R type: install.packages("EBImage", repos="http://R-Forge.R-project.org")

Version: 9.9.9 | Last change: 2009-09-10 20:08:19+02 | Rev.: 1645