[Bioc-devel] Invitation to the bioC developers Meeting in Sea ttle Mon 15 Aug

[Vincent Carey 525-2265]

>
> I'd be happy to follow your suggestions on how to make the package fit more
> with affy-type packages (obvious things is creating subsettabble
> exprset-like object, possibly methods) for the next release. anything else
> that you have in mind? are you suggesting combining three packages? i am
> open to this but it would obviously depend on the other authors.

We want to reduce the complexity that users and developers face
when approaching the system.

-- The packages should distinguish
themselves through high-level documentation/naming so that users
can decide easily which to use.
-- If two packages do very similar
things it would be good for the developers to talk to one another
and decide how to reduce needless complexity, either by amalgamating
the packages or dividing up the intersection so that there
is no overlap.
-- If packages define containers for high-throughput
data structures that are similar to exprSets (GxN assay results,
Nxp phenodata), developers should consider how to simplify conversions.
-- If packages define annotation containers, there should be some
consideration of how the annotation processes of well-established
workflows like affy/annaffy could be emulated.

Any changes should be made keeping in mind the
need for a deprecation period when packages drop functionality.

>
> jane
>
>
> ######################################################
> Jane Fridlyand
> Assistant Professor of Epidemiology and Biostatistics
> Center for Bioinformatics and Molecular Biostatistics
> UCSF Comprehensive Cancer Center
>
> Office: 2340 Sutter str., N224, SF, CA 94114
>
> Tel: 415-476-0168
> Fax: 415-502-3179
>
> ######################################################
>
>
> -----Original Message-----
> From: bioc-devel-bounces at stat.math.ethz.ch
> [mailto:bioc-devel-bounces at stat.math.ethz.ch] On Behalf Of Jeff Gentry
> Sent: Friday, August 05, 2005 11:26 AM
> To: bioc-devel at stat.math.ethz.ch
> Subject: Re: [Bioc-devel] Invitation to the bioC developers Meeting in
> Seattle Mon 15 Aug
>
>
>
> On Fri, 5 Aug 2005, Furge, Kyle wrote:
> > aCGH, DNAcopy, GLAD all use different, internally defined formats for
> > data storage. In addition, feature annotations are stored in separate
> > formats rather then annotation environments. Currently, the convert
> > package does not handle the aCGH, DNAcopy, or GLAD data or annotation
> > formats. I do not want to speak for the original author or the authors
> > of these packages, but in this example, it is worth requiring coerce
> > methods for these (and other) formats into exprSets/annotation
> > environments at the package acceptance stage?
>
> IIRC, the convert package showed up chronologically before the three
> packages that you mentioned - which would explain why it does not handle the
> other three.  At the same time it demonstrates the problem of keeping
> packages up to date with the state of the art in other packages as well.  I
> know I'm guilty of this myself but often package authors/maintainers are not
> aware of changes in other packages which are relevant to their own, and this
> can be a problem.
>
> In a case like the one you describe, where you've personally identified a
> situation that seems like it would make sense to update one (or
> more) packages, IMO the thing to do is at the very least to contact the
> appropriate maintainers and raise this issue - or even better to develop the
> appropriate code/patches to those maintainers.
>
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