[Bioc-devel] bibtex support?

Goeman, J.J. (MSTAT) J.J.Goeman at lumc.nl
Thu Oct 12 15:59:47 CEST 2006

 Hi all,

Does anybody have experience with using bibtex in vignettes? In the
latest version of my package I switched to bibtex for managing the
citations in the vignette of my package, including a .bib file in
inst/doc. This seemed to work fine when I tested it myself. But in the
final release vignette I see all my references replaced by question
marks :-(.

Is bibtex at all supported by the build process? 



-----Oorspronkelijk bericht-----
Van: bioc-devel-bounces at stat.math.ethz.ch
[mailto:bioc-devel-bounces at stat.math.ethz.ch] Namens Sean Davis
Verzonden: woensdag 11 oktober 2006 18:14
Aan: bioc-devel at stat.math.ethz.ch
Onderwerp: Re: [Bioc-devel] RFC for a container for ChIP-chip data

On Wednesday 11 October 2006 12:53, Vincent Carey 525-2265 wrote:
> I am working on an experimental data package for the Harbison
> (PMID 15343339) yeast regulatory code paper.
> the assay data can be looked at either in a gene-centric way (e.g.,
> reporters are genes; most convenient, but some ambiguity) or more
> literally using the intergenic region, for which we have sequence
> information.  the intergenic regions are the things that are
> actually spotted.
> my plan at the moment -- define a ChIPset class that extends
> eSet; the AssayData will probably have accessor brats (for
> binding ratios, not exprs), and i will try to set up featureData
> to have some information on associated intergenic region for
> a gene-centric representation of the assay.  The phenoData will
> give information on the TFs that were chipped for each AssayData
> column
> any concerns with this plan?  any other formats for proprietary
> ChIP-chip data that I don't know about but should?


This looks good for non-tiling Chip-chip data, but not for tiling or 
promoter-tiling chips which are rapidly becoming the standard (?) for 
performing chip-chip analysis.  I would vote for making some distinction

between gene-based chip-chip data and tiling/promoter-based chip, as the

analysis methods and featureData are quite distinct from PCR-product
arrays.  This is probably just a naming thing, but I think ChIPset
different things to different people.  Or, if you go with ChIPset, I
guess a 
TilingChIPset could be created?  I'm not proposing a solution, but just 
pointing out that to many people, ChIP-chip data will imply tiling-array
with genomic locations, etc. and to others it will not.


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