Also note that you can easily map your GenBank IDs to GO IDs or a host of other IDs using biomaRt. Best, Jim Sean Davis wrote: > > > On 8/9/06 3:02 AM, "adlai burman" <fsajb4 at="" uaf.edu=""> wrote: > > >>The GO packages seem to rely solely on LocusLink ids but there are a >>host of onboard affy translators. Now LL seems to be deprecated and I >>don't use affymetrix. > > > Locuslink has simply been replaced by Entrez Gene. For nearly all intents > and purposes, Locuslink still exists, but has the name Entrez Gene. So, > when you read about Locuslink-based analyses, these are still appropriate > and possible. > > >>I have thousands of genes which I would love to >>continue using with BioC. Does anyone know of a mapping somewhere where >>I can batch convert gb nums or gene symbols in a way that R's GO >>packages will accept. Thanks in advance. > > > The AnnBuilder package is the way to build an annotation package for your > genes. It takes genbank ids and makes an annotation package for your array > that you can then use for downstream analyses. > > Alternatively, there are several online resources that allow you to do GO > analyses using genbank IDs. For example, the DAVID/EASE system > (http://david.niaid.nih.gov/david) supports genbank IDs as input. > > Finally, there are tools to convert your genbank accessions to more useable > IDs, like Entrez Gene (Locuslink) IDs. For example, Stanford Source ( > http://source.stanford.edu/cgi-bin/source/sourceSearch) can convert between > genbank IDs and multiple gene identifiers. > > Sean > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.