[BioC] RE: Bioconductor Digest, Vol 9, Issue 28

Yuk Fai Leung YFLeung at cgr.harvard.edu
Thu Nov 20 18:12:40 MET 2003

I would love to see a comprehensive manual like that. It would be very
helpful for biologists. And I believe it is better to disseminate this
manual online rather than as a printed text.

Before this, it would be nice to have a vignette that contains a flowchart
of a typical microarray analysis steps and the applicable libraries like the
one in the short courses for the time being. The chart should be followed by
the short descriptions of the functionalities of the libraries. Then one can
have a quick overview of the bioconductor libraries in just one vignette,
and can choose the suitable library for a particular analysis without
browsing through all the vignettes.

Yuk Fai Leung
Bauer Center for Genomics Research
Harvard University
7 Divinity Avenue
Cambridge, MA 02138
Tel: 617-496-7134
Fax: 617-495-2196
email: yfleung at cgr.harvard.edu; yfleung at genomicshome.com
URL: http://genomicshome.com

> ------------------------------
> Message: 5
> Date: Thu, 20 Nov 2003 09:31:27 +1100
> From: Gordon Smyth <smyth at wehi.edu.au>
> Subject: RE: [BioC] bioconductor
> To: "Warnes, Gregory R" <gregory_r_warnes at groton.pfizer.com>
> Cc: "'rossini at u.washington.edu'" <rossini at u.washington.edu>,	Roger
> 	Vallejo <rvallejo at psu.edu>, bioconductor at stat.math.ethz.ch
> Message-ID: < at imaphost.wehi.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> At 02:39 AM 20/11/2003, Warnes, Gregory R wrote:
> >We talked about this at the BioCBUG meeting a couple of weeks ago.  The
> web
> >site does have clear instructions for *installing* Bioconductor, it is
> just
> >not clear what to do once it is installed.
> >
> >I think that the necessary documentation is available, but it is
> fragmented:
> >
> >1) It is not clear from the web site what documentation you need to read
> to
> >get started.
> >2) None of the vignettes that I've looked at show a complete analysis
> >session from start to finish.
> I think the limma vignette does this.
> By the way, I think your suggestions are great, and I'd dearly like a
> better overview intro to BioC, but fulfilling all the asks below would
> fill
> a two volume book and would make the authors famous!
> Gordon
> >[I think the reason for this is that the people writing the vignettes are
> >the *package* authors and they have slightly different interests from
> >*consumers*]
> >
> >I would suggest
> ...

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