[Bioc-devel] ANN: BioC Developer's Meeting/agenda/discussion

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Sun Jul 17 19:47:22 CEST 2005

> > > >    (or competing with) each other.
> > >
> > > Yes, the task view catalog that I have established will help identify
> > > these competitions more conveniently.  I will shortly post links to
> > this catalog.
> >
> >The first task view rendering can now be seen at
> >http://www.biostat.harvard.edu/~carey/top.html
> >
> >comments welcome.  this was a fairly haphazard construction
> >of topic-set and mapping to packages.
> Are you trying to put each package into one and only one category? I think

definitely not --  but that is a limitation of this first attempt

> that this approach tends to emphasis fragmentation rather than unity and
> doesn't do justice to packages with virtual integration. Topics like
> "Bayes", "linear modelling", "factorial design", "differential expression"
> and "multiple testing", for example, don't split into non-overlapping
> topics. Rather they are all aspects of the same thing. Pre-processing and
> normalization is somewhat more separate, but even this interacts deeply
> with the same topics.
> I suggest that a grouping into larger and not mutually exclusive groups
> might be more helpful.
> Here are some specific problems:
> The limma package isn't mentioned under "Bayesian", "FactorialDesigns",
> "TimeSeries" or "MultipleTesting", even though it is probably the most used
> package in each of these categories.
> Limma isn't mentioned anywhere in any of the Preprocessing categories,
> although it is one of the most used packages for non-affy pre-processing.
> The preprocessing package arrayMagic package, for example, calls limma
> functions to do normalization and pre-processing.
> How are "ErrorModels" different from statistical models used to assess
> differential expression? The LPE and plgem packages should surely get a
> mention under differential expression rather than here. The LPE package is
> very similar in spirit to the empirical Bayes approach for differential
> expression, and should be grouped somewhere with packages like limma,
> EBayes, siggenes etc.
> twilight is another package which seems to me to be doing differential
> expression, but is currently only listed under "MultipleTesting".
> What sort of graphics is included under "Visualization"? Many of the
> packages with pre-processing functionality including plotting functions,
> including marray, limma, arrayMagic.
> Gordon

all that you say is true.  i will soon have the ability
for a package to lie in indefinitely many views.  i want to
hear more dialogue on how the view set can be made more
faithful to creators' intentions, and on which packages
should be associated with which views.

ultimately the view association efforts have to go back
to the developers, with curation at the repository level.
you'll be able to say which views you want your packages
to be associated with, and with what comments.

the metadata about a package that is presented with a
view should vary from view to view.  this is a job the
maintainer/developer should think about.  as you say,
limma can be used for preprocessing and for visualization,
but the comments associated with the view entry for each
of these should be specific to the view.  (i don't have a
comment-associating mechanism yet, but we need one)

this is very early but could move rapidly to something useful
if we do it well.

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