Hi All, I have a simple problem that I can't seem to solve. I am using R 2.4.0 on windows. I am trying to get the GO Terms of a list of GO IDs using the following code. The list of GOIDs is in a file labelled SDGO.txt, which is a single column text file with no header. >library(GO) >SDGO<-read.table("SDGO.txt", header=F) >summary(SDGO) V1 GO:0000075: 1 GO:0000375: 1 GO:0000377: 1 GO:0000398: 1 GO:0001503: 1 GO:0001505: 1 (Other) :134 >apply(SDGO, 1, GOTERM) Error in get(x, envir, mode, inherits) : variable "GOTERM" of mode "function" was not found I am sure I am way off in this code since I am a beginner of R and Bioconductor but I will appreciate any help? Best, Mete

First, your R, and hence your Bioconductor packages are a year out of date, so you should update them. Mete Civelek wrote: > Hi All, > > I have a simple problem that I can't seem to solve. I am using R 2.4.0 on > windows. I am trying to get the GO Terms of a list of GO IDs using the > following code. The list of GOIDs is in a file labelled SDGO.txt, which is > a single column text file with no header. > > >library(GO) > > >SDGO<-read.table("SDGO.txt", header=F) > > >summary(SDGO) > V1 > GO:0000075: 1 > GO:0000375: 1 > GO:0000377: 1 > GO:0000398: 1 > GO:0001503: 1 > GO:0001505: 1 > (Other) :134 > > >apply(SDGO, 1, GOTERM) > Error in get(x, envir, mode, inherits) : variable "GOTERM" of mode > "function" was not found why do you think that is what you should do? something more like mget(SDGO[,1], GOTERM) will be more appropriate or sapply(SDGO[,1], getGOTerm) would be another alternative > > I am sure I am way off in this code since I am a beginner of R and > Bioconductor but I will appreciate any help? > > Best, > > Mete > > _______________________________________________ > 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