Question: Bioconductor 2.4 is released
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gravatar for Bob Treder
10.4 years ago by
Bob Treder10
Bob Treder10 wrote:
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]]
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ADD COMMENTlink modified 10.4 years ago by mondtanzmond10 • written 10.4 years ago by Bob Treder10
Answer: Bioconductor 2.4 is released
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gravatar for Steve Lianoglou
10.4 years ago by
Denali
Steve Lianoglou12k wrote:
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
ADD COMMENTlink written 10.4 years ago by Steve Lianoglou12k
Answer: Bioconductor 2.4 is released
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gravatar for mondtanzmond
10.4 years ago by
mondtanzmond10
mondtanzmond10 wrote:
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 > > >
ADD COMMENTlink written 10.4 years ago by mondtanzmond10
Hi, I wanted to clarify the GEO - ArrayExpress content discussion. To date ArrayExpress and GEO have no formal data exchange agreement to date for array based data. ArrayExpress imports GEO single channel data on commercial platforms by converting SOFT files into MAGE-TAB and also some two colour data. MAGE-ML is a deprecated format for ArrayExpress - we still accept submissions but we do not encourage new pipelines for example. Where GEO = GEO data sets (GDS) these are re-curated by ArrayExpress, for GSE these are simply imported. We do reject some datasets based on data file fails etc. If people would like data to be in AE that's not been curated which originates with GEO this can be requested. We are working towards a data exchange agreement for high throughput sequence data as the short read archives at NCBI and EBI already have such an agreement, and we hope to have something in place soon and data exchange working, thanks Helen
ADD REPLYlink written 10.4 years ago by Helen Parkinson20
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