Thomas Girke wrote: > I would go for the solution that supports a one-to-many relationship > for the probe-to-locus mappings. This way there is no information loss. > The problem with that approach is that it will break an awful lot of downstream code that believes that these are one-to-one mappings. We really would need a full release cycle (starting in early October) to get such a change to work and to minimize the likely negative effects. We would also like to be sure that there are good reasons for the one-to-many result, it is problematic for other reasons as well. best wishes Robert > Thomas > > On Mon 08/14/06 23:25, Nianhua Li wrote: >> Hi, Tine, Bjorn, Thomas and other Arabidopsis experts, >> >> Thanks a lot for the feedbacks. I will get the update done this week if you >> could help me to solve the following problem :P >> >> In TAIR's probe-to-locus mapping file, for example >> ftp://ftp.arabidopsis.org/home/tair/ >> Microarrays/Affymetrix/affy_ATH1_array_elements-2006-07-14.txt >> >> some probesets are mapped to >= 1 locus. However, in annotation packages >> ath1121501 and ag, all annotations (e.g. agCHRLOC, agENZYME) are indexed by >> probeset identifier. It assumes a one-to-one mapping between probeset and gene, >> so that the annotation to a gene is the annotation to a probeset. >> >> How to handle the one probeset to multiple locus mappings? I can think 3 >> possible solutions: >> 1. pick the "best" locus, but how? >> 2. mix the annotations to all mapped locus together >> 3. set to NA >> >> Any suggestions are highly appreciated. Many thanks! >> >> nianhua >> >> _______________________________________________ >> 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 >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Nianhua, I guess in this case, I'd support your second solution: >> 2. mix the annotations to all mapped loci together In the future it may make a lot of sense to support one-to-many relationships on this level. I bet there are a lot of chips from other organisms where a considerable fraction of probe sets maps to several genes. Thanks again for doing this! Best, Thomas On Wed 08/16/06 09:42, Tine Casneuf wrote: > But to me it is hard to think of a way to choose the 'best' locus that > is detected by a probeset. And also if you pick 1 of them, it appears as > if only 1 is detected by this probeset, while actually there are more. > There are I presume not many cases where a measure from these probesets > are useful, so you might as well annotate it with 'multiple'. > > tine > > > Robert Gentleman wrote: > > >Thomas Girke wrote: > >> I would go for the solution that supports a one-to-many relationship > >> for the probe-to-locus mappings. This way there is no information loss. > >> > > > > The problem with that approach is that it will break an awful lot of > >downstream code that believes that these are one-to-one mappings. We > >really would need a full release cycle (starting in early October) to > >get such a change to work and to minimize the likely negative effects. > >We would also like to be sure that there are good reasons for the > >one-to-many result, it is problematic for other reasons as well. > > > > > > best wishes > > Robert > > > > > > > >> Thomas > >> > >> On Mon 08/14/06 23:25, Nianhua Li wrote: > >>> Hi, Tine, Bjorn, Thomas and other Arabidopsis experts, > >>> > >>> Thanks a lot for the feedbacks. I will get the update done this > >week if you > >>> could help me to solve the following problem :P > >>> > >>> In TAIR's probe-to-locus mapping file, for example > >>> ftp://ftp.arabidopsis.org/home/tair/ > >>> Microarrays/Affymetrix/affy_ATH1_array_elements-2006-07-14.txt > >>> > >>> some probesets are mapped to >= 1 locus. However, in annotation > >packages >> ath1121501 and ag, all annotations (e.g. agCHRLOC, > >agENZYME) are indexed by > >>> probeset identifier. It assumes a one-to-one mapping between > >probeset and gene, > >>> so that the annotation to a gene is the annotation to a probeset. > >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" locus, but how? > >>> 2. mix the annotations to all mapped locus together > >>> 3. set to NA > >>> > >>> Any suggestions are highly appreciated. Many thanks! > >>> > >>> nianhua > >>> > >>> _______________________________________________ > >>> 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 > >>> > >> > > > -- Thomas Girke, Ph.D. 1008 Noel T. Keen Hall Center for Plant Cell Biology (CEPCEB) University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437