Hi,


I have got an error while i have been running goseq R package using UCSC
known gene ID such numbers, 1,2,...27315.(27181 genes).

When i computed pwf. it was fine. but, In getgo function, there is an error
message like below:

would you plz look at it and let me know what is wrong with it?

************************************************************************************************
> head(genes)
1 2 3 4 5 6
0 0 0 0 0 0
> str(genes)
 Named int [1:27181] 0 0 0 0 0 0 0 0 0 0 ...
 - attr(*, "names")= chr [1:27181] "1" "2" "3" "4" ...


> pwf = nullp(genes,"mm9","knownGene")
Loading mm9 length data...
> getgo(genes,'mm9','knownGene')
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Error in getgo(genes, "mm9", "knownGene") :
  Couldn't grab GO categories automatically.  Please manually specify.
In addition: Warning message:
replacing previous import ‘summary’ when loading ‘IRanges’

**************************************************************************************************

I will be awaiting the reply from you!


Thanks in advance, sunghee-

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