I would like to use the getPMID function in the package "annotate" but am working data that I only have gene ID's for. Is there a way to make this work? Mark Mark W. Kimpel MD Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202

On Tue, Sep 28, 2004 at 02:20:57PM -0500, Kimpel, Mark W wrote: > I would like to use the getPMID function in the package "annotate" but > am working data that I only have gene ID's for. Is there a way to make > this work? You need to have something that maps to something that is known (what is a gene ID?), if you can get to UniGene or LocusLink etc, then there are many ways (both in Bioconductor and in many other resources) to map from those to PubMed. LocusLink is among the more common. For example, if you are using human genes once you get to LocusLink IDs you can use the humanLLMappings package to get to PMID Robert > > Mark > > Mark W. Kimpel MD > > Department of Psychiatry > Indiana University School of Medicine > Biotechnology, Research, & Training Center > 1345 W. 16th Street > Indianapolis, IN 46202 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

Have you considered making an annotation package for your data using AnnBuilder? What gene ID's do you have? Sean On Sep 28, 2004, at 3:20 PM, Kimpel, Mark W wrote: > I would like to use the getPMID function in the package "annotate" but > am working data that I only have gene ID's for. Is there a way to make > this work? > > Mark > > Mark W. Kimpel MD > > Department of Psychiatry > Indiana University School of Medicine > Biotechnology, Research, & Training Center > 1345 W. 16th Street > Indianapolis, IN 46202 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor