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

Jeff Gentry jgentry at jimmy.harvard.edu
Fri Aug 5 20:26:11 CEST 2005

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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