[Bioc-devel] affy-revised

Laurent Gautier lgautier at altern.org
Wed Nov 17 21:41:43 CET 2004


   During the last months, I did a significant rewrite of the affy
package (well, almost a complete rewrite from scratch), in the light of
the limitations discovered, things there just not right, oddities in the
names, discussions I participated to or just followed silently
(with people on this list, or package users).
This new packages works with the class 'CdfEnvAffy' (package 'altcdfenvs').

Some(*) features are:
- use the class 'eSet' in Biobase (supplementary methods for this
class missing in Biobase are included in this pack).
- the use of 'eSet' as a parent class for the new AffyBatch let one use
pointer-like-sort-of-thing-with-environments (and lower the memory usage)
- The slot for CDF envs can now be a cdfenv name (like it is now), or
directly a AffyCdfEnv (defined for the moment in altcdfenvs). Subsetting
on probes now works (and a CdfEnv is created on the fly); this allows
things like PM-only AffyBatches (hence, half the memory usage). This can
be done directly when reading the raw data.
- Functions exist to register/unregister pre-processing methods. This
will help to have something more robust than what is currently in
'affy', and will (hopefully) help to migrate to sealed namespace in the
- reading subsets of CEL files on the fly
- Probe types can be more than only "pm" or "mm" (one can define new types.)
- interface to have preprocessing functions at the probe set level or at
the whole chip level
- missing documentation :)
- still uses some functions in 'affy' (to avoid uncessary code
duplication for the moment)
- already quite some documention
- easier to adapt the pack to other oligonucletide chips (i.e.,

(*: the design tries to make a lot of things that are not explicitely
detailed possible, but as always it cannot be perfect for everything).

As it is the pack lacks partly documentation, but the good thing is
that anyone with knowledge of the current 'affy' package should figure 
out things easily.

Trying 'example(expressor)' or the main (and incomplete) vignette are
good places to start.

Oops, I almost forget. If some want to play with it, the pack is called
'affyr' (affy-revised) and is available on the Subversion repository.

That's it.


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