[Bioc-devel] affy development - was: RFC: xy2i and i2xy in *cdf packages

Seth Falcon sfalcon at fhcrc.org
Tue Mar 27 16:45:20 CEST 2007

Wolfgang Huber <huber at ebi.ac.uk> writes:

> Hi Henrik, Benilton, Rafa,
> who has the energy to do this and how does this concord with the work on
> oligo? Is oligo intended to replace affy (and if yes, when)? If yes, I
> am not sure it would be worthwhile to spend much time improving affy,
> and we'd just maintain it with existing functionality for a few more
> releases. If no, then of course, further developing affy is an important
> project.

My understanding of where things are moving is:

- The oligo package will replace the affy package within 1-2 releases.

- SQLite-based annotation packages will replace environment-based
  packages.  These will include probe and CDF data along with
  annotation data in a single package.  However, the first batch of
  SQLite-based packages won't include probe and CDF info.

I think some of the design ideas that came up in this thread are good
ones, but clearly we need to focus effort where it will be most useful.
And with the SQLite-based packages, all of the interfaces will be
moderated by one or more S4 classes.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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