[BioC] simLL method in GOstats

[Robert Gentleman]

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 at cbm.bio.uniroma2.it
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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