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

Seth Falcon sfalcon at fhcrc.org
Wed May 9 00:08:35 CEST 2007

"Allen Day" <allenday at gmail.com> writes:

> ---------- 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.

Hmm, either you forgot to attach or something else went wrong, but I
don't think any patch was attached or included.  At least for
discussion you can just put the patch inline.

> affyPLM's fitPLM() cannot return a PLMset unless these
> patches are applied.

It would help to have small example case that demonstrates the issue.

> 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.

Actually, it is the other way around.  The phenoData class is
deprecated and AnnotatedDataFrame is its replacement.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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