[Bioc-devel] eSet classes

Henrik Bengtsson hb at stat.berkeley.edu
Wed Jun 27 17:45:53 CEST 2007

Hi Pierre,

I guess your question concerns development and maintenance of your new
code/package.  I would suggest to use as basic data types (e.g.
vectors, matrices, lists) as possible for the inner/core
implementation of your algorithm(s) and then provide wrapper functions
for more complex structures (e.g. eSet).  The basic data types in R
have been around from day one and will remain until the very end,
whereas other structures (classes) tend to come and go.

This will make it easier for you to maintain and update you algorithm
and add support for new structures when they get around.  It will also
make it easier for others to add support for their structures (without
necessarily having to wrap them up in more complex structure first).
It will also make it easier for others to port your algorithm to other
languages or implement a native-code implementation.

So, keep it simple and add on top of that.



On 6/25/07, Laurent Gautier <lgautier at gmail.com> wrote:
> Hi Pierre,
> My understanding is that the eSet class and friends
> are here to stay... until there is the need to have something better.
> The project is evolving, and this might mean that there is a need to
> keep up with the changes.
> Backward compatibility is tried as much as possible, and when not possible
> a "transition period" generally exists (and when this is the case
> convenience functions to "upgrade" existing instances of a class have
> been provided in the past).
> Planned changes are generally discussed at:
> http://wiki.fhcrc.org/bioc/Core_Bioconductor_Classes_Discussion
> http://wiki.fhcrc.org/bioc/Core_Bioconductor_Classes_Discussion/FeatureLevelData
> (and there have not been many edits for a year now).
> In any case, using "core" classes is probably a good thing to do for at least
> the following reasons:
> - lower your effort (frees you from writing/supporting features
> already in the code packages)
> - facilitates learning for users and developers (similar underlying classes)
> - increased usage of the core classes, and feedback on problems and/or
> wished features leading improved core classes
> Hoping this helps,
> Laurent
> 2007/6/25, Pierre Neuvial <pierre.neuvial at curie.fr>:
> > Hello,
> >
> > Our group has already contributed two R packages to Bioconductor for CGH-array data analysis (MANOR and GLAD). We are currently developping other methods for DNA microarray analysis, and are considering using standard Biobase classes (eSet, ExpressionSet, SnpSet) to implement new packages.
> >
> > My question regards stability of these classes: have major changes to eSet classes been planned in the short or medium term ? If so, will ascending compatibility be
> > guaranteed ?
> >
> > Thanks for your help,
> >
> > Pierre.
> >
> > _______________________________________________
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> >
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