John: One more question to bother you. I have GO_1.5.1 installed. But GOMFOFFSPRINGS is not part of the environment variable; neither is GOLOCUSID. See below: > get("GO:0003700", OFFSPRING) Error in get("GO:0003700", OFFSPRING) : Object "OFFSPRING" not found > GO <environment: 020372e8=""> > GOMFOFFSPRINGS Error: Object "GOMFOFFSPRINGS" not found > GOMFCHILDREN <environment: 02e1adf0=""> > GOLOCUSID Error: Object "GOLOCUSID" not found > Any suggestions? Thanks! Simon ----- Original Message ----- From: "John Zhang" <jzhang@jimmy.harvard.edu> To: <simon.lin@duke.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Friday, July 30, 2004 2:57 PM Subject: Re: [BioC] GOstats: > > >How to find all the off-springs (not only direct children) of a GO term, say > >"GO:0003700"? > > >library(GO) > >get("GO:0003700", GOMFOFFSPRING) > [[1]] > [1] "GO:0003705" > > > >And how to find all the LocusLink IDs associated with these GO terms? > >Take these two questions together, I want to find all the LL-IDs associated > >with a GO node at certain level. > > > mget(unlist(get("GO:0003700", GOMFOFFSPRING)), GOLOCUSID) > IDA IDA IDA IDA IEA NAS NAS NAS NR TAS TAS TAS TAS > 17268 18771 20473 81646 25714 1050 31883 9569 7020 17877 17878 17927 17928 > TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS > 2034 2494 3091 3394 4617 463 4654 4784 5813 5989 5991 7023 > > > > > >I read the vignettes, but am not sure on how to do the above. > > > >Thanks! > > > >Simon > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > >

Simon, The reason you are not getting the correct result is because of typos. You did: get("GO:0003700", OFFSPRING) Jianhua did: get("GO:0003700", GOMFOFFSPRING) ^^^ In addition, there is no such thing as GOMFOFFSPRINGS, which is why that environment was not found. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Simon Lin" <simon.lin@duke.edu> 07/30/04 6:47 PM >>> John: One more question to bother you. I have GO_1.5.1 installed. But GOMFOFFSPRINGS is not part of the environment variable; neither is GOLOCUSID. See below: > get("GO:0003700", OFFSPRING) Error in get("GO:0003700", OFFSPRING) : Object "OFFSPRING" not found > GO <environment: 020372e8=""> > GOMFOFFSPRINGS Error: Object "GOMFOFFSPRINGS" not found > GOMFCHILDREN <environment: 02e1adf0=""> > GOLOCUSID Error: Object "GOLOCUSID" not found > Any suggestions? Thanks! Simon ----- Original Message ----- From: "John Zhang" <jzhang@jimmy.harvard.edu> To: <simon.lin@duke.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Friday, July 30, 2004 2:57 PM Subject: Re: [BioC] GOstats: > > >How to find all the off-springs (not only direct children) of a GO term, say > >"GO:0003700"? > > >library(GO) > >get("GO:0003700", GOMFOFFSPRING) > [[1]] > [1] "GO:0003705" > > > >And how to find all the LocusLink IDs associated with these GO terms? > >Take these two questions together, I want to find all the LL-IDs associated > >with a GO node at certain level. > > > mget(unlist(get("GO:0003700", GOMFOFFSPRING)), GOLOCUSID) > IDA IDA IDA IDA IEA NAS NAS NAS NR TAS TAS TAS TAS > 17268 18771 20473 81646 25714 1050 31883 9569 7020 17877 17878 17927 17928 > TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS TAS > 2034 2494 3091 3394 4617 463 4654 4784 5813 5989 5991 7023 > > > > > >I read the vignettes, but am not sure on how to do the above. > > > >Thanks! > > > >Simon > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor