Hi Mikko, you'll be able to get oligo from the devel branch soon. if you get your files before, please let me know, so i can provide you the packages. b. On Mon, 17 Oct 2005, Mikko Arvas wrote: > > Hi, > > I thought the Oligo package would be coming with this release. I'll be > getting set of xys format files from Nimblegen this week and would have > liked to give it a go. Can I get it from somewhere else? > > All the best, > Mikko > > At 16:56 14.10.2005 -0700, Seth Falcon wrote: >> We are pleased to announce the release of Bioconductor 1.7. This >> release includes 17 new packages and many improvements and bug fixes >> to existing packages. >> >> Please visit http://www.bioconductor.org for details and downloads. >> >> Contents >> ======== >> >> - Release Highlights >> - Getting Started With Bioconductor 1.7 >> - Known Issues >> - 17 New Packages >> >> >> Release Highlights >> ================== >> >> - Rgraphviz is now available as a binary package for Windows >> >> - Annotation data packages now include protein information from IPI >> (see the PFAM and PROSITE environments in the data packages). >> >> >> Getting Started With Bioconductor 1.7 >> ===================================== >> >> To get started with Bioconductor 1.7, please: >> >> - Install R 2.2.0. Bioconductor 1.7 has been designed expressly for >> this version of R. >> >> - Follow the instructions here: >> http://www.bioconductor.org/docs/install-howto.html >> >> >> Known Issues >> ============ >> >> - The following packages are not currently available for Windows: >> affxparser biomaRt GeneR GeneTraffic >> iSPlot KEGGSOAP maDB MANOR >> msbase pgUtils RdbiPgSQL rhdf5 >> RMAGEML SAGElyzer SBMLR stam >> widgetInvoke >> >> - The following packages are not currently available for OS X: >> aCGH edd RdbiPgSQL rhdf5 >> RMAGEML xcms >> >> - The genbank() function in package annotate is broken. The CGI >> script it was accessing at NCBI appears not to be functioning. You >> will see a message like:: >> >> parser error : Start tag expected, '<' not found >> Content-Type: text/html; charset=UTF-8 >> >> - The hexbin package is unable to execute its vignette on Windows. A >> plot method fails giving an error message about -Inf, Inf xlim. >> >> - The golubEsets dataset is temporarily unavailable, it will be fixed >> next week. >> >> >> 17 New Packages >> =============== >> >> affxparser >> Title: Affymetrix File Parsing SDK >> Author: James Bullard, Kasper Daniel Hansen >> >> affyQCReport >> Title: QC Report Generation for affyBatch objects >> Author: Craig Parman, Conrad Halling >> >> clusterStab >> Title: Compute cluster stability scores for microarray data >> Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin >> >> diffGeneAnalysis >> Title: Performs differential gene expression Analysis >> Author: Choudary Jagarlamudi >> >> externalVector >> Title: Vector objects for R with external storage >> Author: Saikat DebRoy >> >> fdrame >> Title: FDR adjustments of Microarray Experiments (FDR-AME) >> Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli >> >> GlobalAncova >> Title: Calculates a global test for differential gene expression >> Author: U. Mansmann, R. Meister >> >> HEM >> Title: Heterogeneous error model for identification of differentially >> expressed genes under multiple conditions >> Author: HyungJun Cho >> >> maSigPro >> Title: Significant Gene Expression Profile Differeneces in Time Course >> Microarray Data >> Author: Ana Conesa, Maria Jos? Nueda >> >> maanova >> Title: Tools for analyzing Micro Array experiments >> Author: Hao Wu <hao at="" jax.org="">, with ideas from Gary Churchill, Katie Kerr >> and Xiangqin Cui >> >> MANOR >> Title: Micro-Array NORmalization >> Author: Pierre Neuvial, Philippe Hup? >> >> mmgmos >> Title: multi-chip modified gamma Model of Oligonucleotide Signal >> Author: Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence >> >> pdmclass >> Title: Classification of Microarray Samples using Penalized Discriminant >> Methods >> Author: James W. MacDonald, Debashis Ghosh, based in part on >> >> reb >> Title: Regional Expression Biases >> Author: Kyle A. Furge and Karl Dykema >> >> simulatorAPMS >> Title: Computationally simulates the AP-MS technology. >> Author: Tony Chiang <tchiang at="" fhcrc.org=""> >> >> SBMLR >> Title: SBML-R Interface and Analysis Tools >> Author: Tomas Radivoyevitch >> >> timecourse >> Title: Statistical Analysis for Developmental Microarray Time Course Data >> Author: Yu Chuan Tai >> >> >> Best Wishes, >> >> + seth >> For the Bioconductor Core Team >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Mikko Arvas > VTT Biotechnology > > Please note new tel/fax number > from start of year 2005. > > e-mail: mikko.arvas at vtt.fi > tel: +358-(0)20-722 5827 > mobile: +358-(0)44-381 0502 > fax: +358-(0)20-722 7071 > mail: Tietotie 2, Espoo > P.O. Box 1500 > FIN-02044 VTT, Finland > > Protein production group's website: > http://www.vtt.fi/bel/bpro/proteinprod/indexe.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Norman this is going to happen this week as Simon Urbanek is traveling and Fritz L. is setting up the new mirroring. I can assure that everything is already in place, tested and working. Just wait a couple of days more. stefano On 17/ott/05, at 12:38, Norman Pavelka wrote: > First of all, congratulations to the whole BioC team for the new > release! > > Secondly, since BioC 1.7 relies on R 2.2, are there any news > regarding when the R 2.2 installer is scheduled to be released for > Mac OS X (in the form of the usual disk image)? I still couldn't > find it on CRAN... Maybe Stefano has any clues? I'd like to avoid > installing it from source... > > Thanks in advance! > > Best, > Norman > > Norman Pavelka > Department of Biotechnology and Bioscience > University of Milano-Bicocca > Piazza della Scienza, 2 > 20126 Milan, Italy > > Phone: +39 02 6448 3556 > Fax: +39 02 6448 3552 > > On 15 Oct 2005, at 12:00, bioconductor-request at stat.math.ethz.ch > wrote: > > >> From: Seth Falcon <sfalcon at="" fhcrc.org=""> >> Date: 15 October 2005 01:56:16 GMT+02:00 >> To: bioconductor at stat.math.ethz.ch, bioc-devel at stat.math.ethz.ch >> Subject: [BioC] ANN: Bioconductor Release 1.7 is available >> >> >> We are pleased to announce the release of Bioconductor 1.7. This >> release includes 17 new packages and many improvements and bug fixes >> to existing packages. >> >> Please visit http://www.bioconductor.org for details and downloads. >> >> >