[Bioc-devel] eSet classes

[Laurent Gautier]

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.
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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