libaffy

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 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 actually doing useful things with them. We have also implemented the MAS5.0 and RMA expression algorithms within this library. Driver applications, including a graphical MAS5/RMA program, are bundled with the libaffy distribution. The purpose of this library is a codebase upon which many different experimental or practical projects could be based.

We have validated libaffy correctness to both the Bioconductor and Affymetrix implementations. There are issues regarding MAS5.0 which are detailed here.

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Documentation

• libaffy HTML Documentation (libaffy.html)
• libaffy PDF Documentation (libaffy.pdf)

Background

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.

Contacts

Andrew Hoerter, Steven Eschrich