GO annotation cannot correctly introduced into R

Question

[citronxu]

Hello,

I'm working recently on GO analysis regarding A.thaliana whose database is not included in GOseq package. Then I downloaded the GO annotation from both gene ontology website and TAIR as DAF file (version 2.0/2.1) and was gonna introduce it into R with function readDAF of mgsa. However, during the reading of both files, error has been returned as follow...

Error in readGAF("~/Downloads/gene_association.tair") : 
  At least one DB object ID has multiple DB object symbols or names in gene ontology annotation file.
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

The error lies on same object has multiple names, is there any argument can bypass this? or I didn't get the right file...many thanks in advance!!

[Fatima]

ftp://ftp.geneontology.org/pub/go/software/utilities/ has a perl code "filter-gene-association.pl" that might do the trick, but I haven't used it personally.