Affymetrix has developed a series of gene chip microarrays that have become increasingly popular in gene expression studies. In order to facilitate the use of these microarrays at the Moffitt Cancer Center, we have developed a C software library for accessing the various file types generated by their software and image capture devices.

libaffy consists of a set of routines for accessing the various file types (DAT, CEL, CDF) and post-processing them using a variety of algorithms, including MAS5.0, RMA, and IRON. The purpose of this library is a codebase upon which many different experimental or practical projects could be based.




Note: Documentation linked here is always built from the latest release tag in the source control repository, and may be out of sync with older versions. Documentation may also be out of date and not reflect newer versions which have not been properly documented yet.


When we first began experimenting with Affymetrix microarrays, much of the useful software for accessing this data from the raw files was not available. The excellent Bioconductor project has been most noticeable in filling that gap. However, we feel that having a library of routines available for public consumption would allow for greater flexibility. In addition, many of the data structures and algorithms have been implemented with an eye both towards readability and performance (particularly memory usage). In this, we feel libaffy succeeds very well.


Welsh et al.; BMC Bioinformatics, 2013. 14:153
Eschrich et al.; Engineering in Medicine and Biology Society, 2008. EMBS 2008. 30th Annual International Conference of the IEEE
Eschrich SA, Hoerter AM; Bioinformatics, 2007. Jun 15;23(12):1562-4


Eric A. Welsh (
Steven A. Eschrich (