The affxparser package (Affymetrix File Parsing SDK)

The affxparser package provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both traditional ASCII- and binary-based files are supported, as well as Affymetrix future binary format "Calvin". The efficiency of the parsing is dependent on whether a specific file is binary or ASCII.

Installation and updates

The main repository for this package is Bioconductor. To install it, do:

source("http://www.bioconductor.org/biocLite.R")
biocLite("affxparser")

source("http://www.braju.com/R/hbLite.R")
hbLite("affxparser")

Help

Always turn to the package help in the first place, especially the package overview help page, i.e.

library(affxparser)
?affxparser

Additional documentation beyond the help pages

H. Bengtsson, Introduction to the affxparser package, Department of Statistics, University of California, Berkeley, May 11, 2006.

• Talk (32 slides): pdf [276kb], png:s [2.5Mb].
• LaTeX source and images: zip [112kb] (if use, please cite).

External links

• Fusion Software Developers Kit (SDK)
• Affymetrix' DevNet Forums (requires login)
• File formats documentation - November 2008