geneplotter - buildChromLoc for arrays with no .db package
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@lavinia-gordon-2959
Last seen 7.7 years ago
Hi, I'd like to use the buildChromLoc function in geneplotter for GenomeWideSnp 6.0 Affymetrix arrays. As there does not appear to be a suitable .db package available for these arrays, I'm looking for any tips/pointers on how to go about this, e.g. I'm guessing one option would be to use the org.Hs.eg.db and map my 6.0 ids back to these locations, or to create a .db package using AnnotationForge. With many thanks for your time, Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com
GO geneplotter GO geneplotter • 757 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.8 years ago
United States
Hi Lavinia, Have you tried using this? http://www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationFor ge/inst/doc/SQLForge.pdf Marc On 12/03/2012 04:57 PM, Lavinia Gordon wrote: > Hi, > I'd like to use the buildChromLoc function in geneplotter for > GenomeWideSnp 6.0 Affymetrix arrays. > As there does not appear to be a suitable .db package available for > these arrays, I'm looking for any tips/pointers on how to go about this, > e.g. I'm guessing one option would be to use the org.Hs.eg.db and map my > 6.0 ids back to these locations, or to create a .db package using > AnnotationForge. > With many thanks for your time, > > Lavinia Gordon > > Senior Research Officer > Quantitative Sciences Core, Bioinformatics > > Murdoch Childrens Research Institute > The Royal Children's Hospital > Flemington Road Parkville Victoria 3052 Australia > T 03 8341 6221 > www.mcri.edu.au > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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