We are trying to use goseq on our yeast data, but there is a problem with the yeast database. I managed to create a pwf object with nullp(), but the next step fails:
> pwf = nullp(gene.vector, "sacCer3", "ensGene") Can't find sacCer3/ensGene length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes. > head(pwf) DEgenes bias.data pwf 15S_RRNA 0 NA NA 21S_RRNA 0 NA NA HRA1 0 564 0.04489934 ICR1 0 3199 0.08983848 LSR1 0 1175 0.06094949 NME1 0 340 0.03602508 > GO.wall = goseq(pwf, "sacCer3", "ensGene") Fetching GO annotations... Error in toTable(get(paste(orgstring, "GO2ALLEGS", sep = ""))) : error in evaluating the argument 'x' in selecting a method for function 'toTable': Error in get(paste(orgstring, "GO2ALLEGS", sep = "")) : object 'org.Sc.sgdGO2ALLEGS' not found >
It seems that org.Sc.sgd.db is missing GO2ALLEGS, called by the goseq script. Any suggestions for a fix or workaround?