Hi Patrick, Can you direct me to any good overall training materials for the bioconductor packages for gene expression analysis? I'm interested primarily in scripts and example data. I've done a fair amount of work with S+ArrayAnalyzer at the GUI level, but want to come up to speed at the command level. Hope all is well with you and family. Thanks, Bob Robert Treder, PhD Sr Consultant TIBCO Spotfire Division 1700 Westlake Ave N, Suite 500 Seattle, WA 98109 Off: (206) 802-2231 Cell: (206) 954-4376 Toll Free: (800) 569-0123 ext. 231 Fax: (206) 283-8691 Email: rtreder@tibco.com <mailto:rtreder@tibco.com> Web: www.insightful.com <http: www.insightful.com=""/> [[alternative HTML version deleted]]

Hi, > Can you direct me to any good overall training materials for the > bioconductor packages for gene expression analysis? I'm interested > primarily in scripts and example data. I've done a fair amount of work > with S+ArrayAnalyzer at the GUI level, but want to come up to speed at > the command level. Start with the "primer" vignette in the affy package: R> library(affy) R> openVignette() Please select a vignette: 1: affy - 1. Primer 2: affy - 2. Built-in Processing Methods 3: affy - 3. Custom Processing Methods 4: affy - 4. Import Methods 5: Biobase - An introduction to Biobase and ExpressionSets 6: Biobase - Bioconductor Overview 7: Biobase - esApply Introduction 8: Biobase - Notes for eSet developers 9: Biobase - Notes for writing introductory 'how to' documents 10: Biobase - quick views of eSet instances Choose (1) Also, for an overview of how to analyze differential expression, see the limma user guide: R> library(limma) R> limmaUsersGuide() Lastly, I've never read it myself, but perhaps the "Bioconductor Caste Studies" book might be valuable: http://www.bioconductor.org/pub/biocases/ HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Bob Treder schrieb: > Hi Patrick, > > > > Can you direct me to any good overall training materials for the > bioconductor packages for gene expression analysis? I'm interested > primarily in scripts and example data. I've done a fair amount of work > with S+ArrayAnalyzer at the GUI level, but want to come up to speed at > the command level. > > > > Hope all is well with you and family. > > > > Thanks, > > Bob > > > > Robert Treder, PhD > > Sr Consultant > > TIBCO Spotfire Division > > 1700 Westlake Ave N, Suite 500 > > Seattle, WA 98109 > > > > Off: (206) 802-2231 > > Cell: (206) 954-4376 > > Toll Free: (800) 569-0123 ext. 231 > > Fax: (206) 283-8691 > > Email: rtreder at tibco.com <mailto:rtreder at="" tibco.com=""> > > Web: www.insightful.com <http: www.insightful.com=""/> > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >