[Bioc-devel] Fwd: [PATCH] affy 1.12.2 affyPLM 1.12.0 interoperability

[bmb at bmbolstad.com]

> ---------- Forwarded message ----------
> From: Allen Day <allenday at gmail.com>
> Date: May 4, 2007 4:32 PM
> Subject: [PATCH] affy 1.12.2 affyPLM 1.12.0 interoperability
> To: bioc-devel at stat.math.ethz.ch
>
>
> see attached.  affyPLM's fitPLM() cannot return a PLMset unless these
> patches are applied.  It appears that it is using an older interface
> (AnnotatedDataFrame in place of phenoData, alternately named MIAME
> member), although I am not really familiar with the history of any of
> this.
>
> -Allen
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>

Note that affyPLM 1.12.0 is designed to work only with the version of affy
in BioC 2.0 in particular 1.14.0 (and also the Biobase from this same
release).

While I can't see your patch I can tell you that I would not expect
affyPLM 1.12.0 to work well with the previous release of BioC software or
vice versa. The general approach of BioC is that we only guarantee (or
least try to promise) that packages in the same stable releast set will
interoperate. There is no guarantee that you can mix and match packages
between releases or between the release and the development stream and
have it all work properly.

Best,

Ben