- When asked in January 2007 Allen suggested people may want to use the "affy" packages in Bioconductor instead (read that email and this email).
- A possible new direction to take these modules could be using them as a bridge between Bioconductor data analyses and various BioPerl object models (i.e. Bio::Seq, Bio::Seq::RichSeq, etc.). Maybe some bioperl-run-based wrappers, bioperl-db adaptors?.
- Christopher Jones has published an article in Bioinformatics about his Microarray perl module in CPAN.
- Another option for working with Affymetrix data files is the Affymetrix Power Tools, as mentioned by Steve Chervitz in this bioperl-l thread.
The latest code
The latest, and not completely tested, code can be viewed here:
You can download it by following the instructions on the main Subversion page. The repository name is bioperl-microarray.