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. Regards, Fai _______ 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@cgr.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com > ------------------------------ > > Message: 5 > Date: Thu, 20 Nov 2003 09:31:27 +1100 > From: Gordon Smyth <smyth@wehi.edu.au> > Subject: RE: [BioC] bioconductor > To: "Warnes, Gregory R" <gregory_r_warnes@groton.pfizer.com> > Cc: "'rossini@u.washington.edu'" <rossini@u.washington.edu>, Roger > Vallejo <rvallejo@psu.edu>, bioconductor@stat.math.ethz.ch > Message-ID: <6.0.1.1.1.20031120092602.02938a88@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 > > ... >

Anybody here using manova? It's powerful and pretty fast, but I'm finding that you can't have more variables than samples (limits its applicability to microarray research). Is there any way around this? Assume dim(eset) 1200 35 transeset<-t(eset) fit<-manova(transeset ~ categories) summary(fit) There is probably a complicated mathematical truth that underlies this limitation--if anybody can shed some light, that would be great. Also, if anyone knows of a quick, free multivariate tool that summarizes all the tests into a single test statistic, that would be much appreciated. Regards, Michael Benjamin, MD Emory University Winship Cancer Institute