Hi Maria, You have not told us about the operating system you are using, nor about versions of packages. I have found the source of the problem. For simLL("10554","10486") the problem is that the gene with GeneID 10486 has no MF GO annotations. And hence we cannot compute a GO graph for MF (I hope you know that is what you are doing for comparison). I have modified the code so that NA is returned in this case. The fix (you can try to fix the R code on your computer) is below or I can provide a new version of the package - but only for Unix; for windows you will need to wait until Monday or Tuesday. Best wishes, Robert ps the fix - in R, for example - but you must do it every time you load the library go: fix(simLL) then in your favorite editor add the lines with +'s shown below g1 = GOGraph(ll1GO, dataenv) g2 = GOGraph(ll2GO, dataenv) + if( length(g1) == 0 || length(g2) == 0 ) + return(NA) sm = match.arg(measure, c("LP", "UI")) On Apr 30, 2005, at 10:49 AM, Maria Persico wrote: > Dear Seth, dear Robert, > > thanks for your answers. > > I have still problems because I couldn't reinitialize goanal(sorry, > I'm a > beginner): > indeed.... >> goanal > [1] "Error: invalid subscript type\n" > attr(,"class") > [1] "try-error" > >> str(goanal) > Class 'try-error' chr "Error: invalid subscript type > " > > > this is the code that doesn't work: >> distances<-numeric(100) >> for (i in 1:100){ > + goanal <- > try(simLL(as.character(hmapr$V1[i]),as.character(hmapr$V2[i]),"MF")) > + if (inherits("gonal", "try-error")) { > + goanal <- as.list() > + #goanal[["sim"]] <- NA > + #print(goanal$sim) > + distances[i]<-NA#goanal$sim > + > + } > + else{ > + > goanal<- > simLL(as.character(hmapr$V1[i]),as.character(hmapr$V2[i]),"MF") > + print(goanal$sim) > + distances[i]<-goanal$sim > + > + } > + > + } > > > Some example where the function fails: > (I'm working with human genes) > The last pair for which I have a distance is simLL("2935","8894") > The pair where simLL fails: >> simLL("10554","10486") > Error: invalid subscript type > > another examples of failures: >> simLL("81608","55339") > Error: invalid subscript type >> simLL("50999","10972") > Error: invalid subscript type >> simLL("50999","10972") > Error: invalid subscript type > > Thanks, > > Maria > > Maria Persico > MINT database, Cesareni Group > Universita' di Tor Vergata, via della Ricerca Scientifica > 00133 Roma, Italy > Tel: +39 0672594315 > FAX: +39 0672594766 > e-mail: maria@cbm.bio.uniroma2.it > > > On Sat, 30 Apr 2005, Robert Gentleman wrote: > >> Hi, >> As Seth said you can use try (or some of the other features of the >> exception handling system). >> Would it be possible to supply me with an example where it fails - it >> might be better to fix the code so that it handles these cases more >> gracefully, >> >> thanks, >> Robert >> >> On Apr 30, 2005, at 4:14 AM, Maria Persico wrote: >> >>> Dear bioconductor mailing list, >>> >>> I have some pairs of genes and I would like to measure their >>> "distances" >>> on the GO molecular function graph. >>> >>> So I wrote this lines of code: >>> >>> distances<-numeric(100) >>> for (i in 1:100){ >>> >>> goanal<- >>> simLL(as.character(hmapr$V1[i]),as.character(hmapr$V2[i]),"MF") >>> print(goanal$sim) >>> distances[i]<-goanal$sim >>> rm(goanal) >>> } >>> >>> where hmapr$V1 and hmapr$V2 are the vectors in which I have the locus >>> link >>> identifiers of my genes. >>> >>> When I run the script, in a few time I obtain >>> "Error: invalid subscript type". >>> >>> I noticed that there are problems with the pair of llID where the >>> script >>> stops. >>> >>> Is there a way to bypass the problem, to jump to the next pair >>> of genes after putting NaN in the distances vector? >>> >>> Thanks a lot, >>> >>> Maria >>> >>> >>> >>> >>> >>> Maria Persico >>> MINT database, Cesareni Group >>> Universita' di Tor Vergata, via della Ricerca Scientifica >>> 00133 Roma, Italy >>> Tel: +39 0672594315 >>> FAX: +39 0672594766 >>> e-mail: maria@cbm.bio.uniroma2.it >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >> +--------------------------------------------------------------------- >> -- >> ----------------+ >> | Robert Gentleman phone: (206) 667-7700 >> | >> | Head, Program in Computational Biology fax: (206) 667-1319 | >> | Division of Public Health Sciences office: M2-B865 >> | >> | Fred Hutchinson Cancer Research Center >> | >> | email: rgentlem@fhcrc.org >> | >> +--------------------------------------------------------------------- >> -- >> ----------------+ >> >> > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+