Question: problem with chromosome location in annotations WAS: search archives and annnotate questions
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gravatar for Diego Diez
13.6 years ago by
Diego Diez750
Japan
Diego Diez750 wrote:
Dear all, I have been building annotation packages for Codelink platform these days and found this problem exist, but only in the human arrays. No chromosome locations are found. The annotations created for both mouse and rat arrays have the corresponding chromosome locations. At the first time I was thinking on a problem with my mapping between codelink ids and genbank ids (recently changed a bit) in the human arrays but now I realize that it could be a more general problem. This is the corresponding information about my system: > sessionInfo() Version 2.3.0 (2006-04-24) i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder RSQLite DBI annotate XML Biobase "1.12.0" "1.10.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7" "1.10.0" I have and old build from Mon Jan 16 06:53:47 2006 that has the corresponding chromosome location but I don't have information about sessionInfo(), only that it was built for R-2.2.0. If you need any other information let me know. Any help on this will be very appreciated. Best regards, Diego. >Why is it that so many probesets are annotated with respect to chromosome and cytoband, but >not to "chromosome location" in the annotation packages? I recently performed an analysis using >rat2302 (ver.1.12.0) and passed the results on to a colleague, who subsequently told me that he >has found locations for quite a few of the probesets with location "zero" at the Affy website. > >I tried to see if this question has been addressed before but ran into the following problems: >1. the search button on the Bioconductor homepage is not working (Firefox 1.5.1). >2. the searchable archives site I used to use has been shut down (http://files.protsuggest.org/cgi->bin/biocond.cgi). >3. I am not sure how to Goggle just the BioC archives (https://stat.ethz.ch/pipermail/>bioconductor/). > >Help in these areas would be appreciated. > >Thanks, > >Mark W. Kimpel MD > > >Official Business Address: >? >Department of Psychiatry >Indiana University School of Medicine >Biotechnology, Research, & Training Center >1345 W. 16th Street >Indianapolis, IN ?46202 >? >Preferred Mailing Address: >? >15032 Hunter Court >Westfield, IN? 46074 >? >(317) 490-5129 Home, Work, & Mobile >1-(317)-536-2730 FAX >
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