I thought this might be of interest. Here's a forwarded message and attachment from Ola Spjuth allowing LIMMA and SMA to work as a BASE (http://base.thep.lu.se) plug-in. Please direct questions to Ola or the BASE mailing list. Lao Lao H. Saal Institute for Cancer Genetics / Herbert Irving Cancer Center College of Physicians & Surgeons, Columbia University 1150 St. Nicholas Ave, Room 302 New York, New York 10032 email: lhs74@columbia.edu tel: +1-212-851-5263 >From: "Ola Spjuth" <ola.spjuth@lcb.uu.se> >To: <basedb-users@lists.sourceforge.net> >Subject: [base] LCB R-Plugins v 0.92 >Organization: Linnaeus Centre for Bioinformatics >X-Mailer: Microsoft Outlook, Build 10.0.2627 >Date: Mon, 29 Sep 2003 17:43:42 +0200 > >I have attached the R: Bioconductor (LIMMA) and SMA plugins v 0.92 created >for the Linnaeus Centre for Bioinformatics including: > > > >base_R.pl Perl-script for executing R-scripts from BASE > >parse.basefile.R Functions for reading/writing BASEfiles within R > >arrayplots.R R-script for constructing various Array plots > >rnorm.R R-script using Bioconductor(LIMMA) >functions to normalize 2ch arrays > >rnorm.betw.arr.R R-script using Bioconductor(LIMMA) functions >to normalize between arrays > >bstat.R R-script using Bioconductor(LIMMA) >functions to rank genes by B-statistics > >bstat.dupcor.R R-script using Bioconductor(LIMMA) functions >to rank genes by B-statistics with duplicate correction (dupcor) > > > >All plugins output HTML-files with plots. Many updates and bug fixes since >last version. Design matrices are imputed as text in plugin. > >See included README.txt for more information and installation >instructions. Still manual installation, I have not investigated the new >plugin devkit. > > > >Use it if you like, send me bug-reports if you like, and please write your >own R-scripts and share with everyone. > > > >Regards, > > > >- - - - - - - - - - - - - - - - - - - > >Ola Spjuth > >ola@crossoverbio.com > ><http: www.crossoverbio.com=""/>www.crossoverbio.com > >www.lcb.uu.se > > > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: R-plugins_lcb_v092.tar.gz Type: application/octet-stream Size: 10285 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030929/56c28727/R-plugins_lcb_v092.tar.obj