[Bioc-devel] bibtex support?

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? 

Jelle

www.msbi.nl/goeman 


-----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

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?

Vince,

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
based 
arrays.  This is probably just a naming thing, but I think ChIPset
implies 
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
data 
with genomic locations, etc. and to others it will not.

Sean

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