Hi 

I'm trying to use topGO to analyse a list of interesting genes generated using the Affy HGU-133plus2 platform but a custom cdf. 

The gene universe is a list of Ensembl transcript ids. I have annotated these with the BP GO using biomaRt 

> head(bio_process_go)
  go_biological_process_id ensembl_transcript_id
1               GO:0007264       ENST00000000233
2               GO:0015031       ENST00000000233
3               GO:0016192       ENST00000000233
4               GO:0006886       ENST00000000233
5               GO:0006810       ENST00000000412
6               GO:0006898       ENST00000000412

and created a list object for feeding to topGO



e.g.

>test1<-unstack(bio_process_go)
> str(test1)
List of 13847
 $ ENST00000000233: chr [1:4] "GO:0007264" "GO:0015031" "GO:0016192" "GO:0006886"
 $ ENST00000000412: chr [1:4] "GO:0006810" "GO:0006898" "GO:0008333" "GO:0015761"
 $ ENST00000000442: chr [1:2] "GO:0006350" "GO:0006355"
 $ ENST00000001008: chr [1:6] "GO:0006457" "GO:0006463" "GO:0006825" "GO:0007566" ...

I have created the named factor which topGO should use to seperate my interesting genes from the list.

e.g.

> str(geneList)
 Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:25068] "ENST00000000233" "ENST00000000412" "ENST00000000442" "ENST00000001008" ...

I then create my topGO data object thus:

GOdata<-new('topGOdata', ontology='BP', allGenes=geneList, annotFUN.gene2GO, gene2GO=test1)

using the annotFUN.gene2GO argument since that's the direction my annotation goes in.

However I get the following error:

Building most specific GOs .....Error in .local(.Object, ...) : 
  argument "annotationFun" is missing, with no default

Can anyone advise on where I'm going wrong?

Thanks

Iain

> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-apple-darwin8.10.1 

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] topGO_1.8.1         SparseM_0.78        GO.db_2.2.0         AnnotationDbi_1.2.0
 [5] RSQLite_0.6-8       DBI_0.2-4           Biobase_2.0.0       graph_1.18.1       
 [9] biomaRt_1.14.1      RCurl_0.9-4        

loaded via a namespace (and not attached):
[1] XML_1.96-0      cluster_1.11.10


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