I have a question regarding GOHyperG function in GOstat. Is it possible to use this function with the Arabidopsis ath1121501 annotation package? The function GOHyperG requires a vector of LocusLink identifiers, however LocusLink identifiers don't seem to be available in the latest ath1121501 package since it is based on data sources from the Tair project (which is a good choice). Is there a way to work around this limitation and use this annotation package with GOHyperG? I have tried to use alternative loci identifiers, but this resulted in the below error message. Here is an example of what I have tried to do: > library(GOstats) > library(ath1121501) > library(GO) > zz1<-as.list(ath1121501ACCNUM) # or any other available mapping > zz2<-unique(unlist(zz1))[1:100] > xx<-GOHyperG(zz2, lib="ath1121501", what="MF") Error in get(x, envir, mode, inherits) : variable "ath1121501LOCUSID" of mode "environment" was not found Error in as.list(getDataEnv("LOCUSID", lib)) : unable to find the argument 'x' in selecting a method for function 'as.list' Thanks, Thomas -- Thomas Girke University of California Riverside, CA 92521

Hi, Not easily. Basically the current mapping is from Entrez Gene IDs to GO. So if you have a different system for going to GO categories you would need to modify the code accordingly. That is sort of the essential piece - how do you go from your IDs to GO categories, after that it is just hypergeometric calculations. Best wishes, Robert Thomas Girke wrote: > I have a question regarding GOHyperG function in GOstat. Is it > possible to use this function with the Arabidopsis ath1121501 > annotation package? The function GOHyperG requires a vector of > LocusLink identifiers, however LocusLink identifiers don't seem to be > available in the latest ath1121501 package since it is based on > data sources from the Tair project (which is a good choice). > Is there a way to work around this limitation and use this annotation > package with GOHyperG? > > I have tried to use alternative loci identifiers, but this resulted > in the below error message. Here is an example of what I have tried to do: > > >>library(GOstats) >>library(ath1121501) >>library(GO) >>zz1<-as.list(ath1121501ACCNUM) # or any other available mapping >>zz2<-unique(unlist(zz1))[1:100] >>xx<-GOHyperG(zz2, lib="ath1121501", what="MF") > > > Error in get(x, envir, mode, inherits) : variable "ath1121501LOCUSID" of mode "environment" was not found > Error in as.list(getDataEnv("LOCUSID", lib)) : > unable to find the argument 'x' in selecting a method for function 'as.list' > > Thanks, > > Thomas >