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

Gordon Smyth smyth at wehi.edu.au
Sun Jul 17 09:44:36 CEST 2005

At 01:33 PM 8/07/2005, Vincent Carey 525-2265 wrote:
> > > 2. Integration of efforts (packages) that are currently duplicating
> > >    (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
>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 
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.


> > card.  I started modifying the R reference card by Tom Short (CRAN/
> > Documentation/Contributed) and
> > will check in a package bcRefcard so that we can do this jointly.
>now checked in at madman/Rpacks -- very little done for the bioc
>card at present.

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