Thanks for your replies Adrian and James.

My data is as before. I construct the topGO data object with:

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

and I get

Building most specific GOs .....Error in .local(.Object, ...) : object "annotFUN.gene2GO" not found

hmm... not so good.

> str(test1[1:10])
List of 10
 $ 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" ...
 $ ENST00000001146: chr [1:7] "GO:0001709" "GO:0007140" "GO:0007283" "GO:0009954" ...
 $ ENST00000002165: chr [1:2] "GO:0005975" "GO:0008152"
 $ ENST00000002829: chr "GO:0007275"
 $ ENST00000003100: chr [1:2] "GO:0055114" "GO:0006508"
 $ ENST00000003302: chr [1:3] "GO:0006511" "GO:0006512" "GO:0008152"
 $ ENST00000004531: chr [1:4] "GO:0006520" "GO:0006810" "GO:0015807" "GO:0006865"

looks ok

> 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" ...

looks ok!

I thought perhaps I had made a fundamental error like a spelling error some where, but pasting in Adrians line made no difference. So I've probably made another error!

Any further advice would be appreciated. 

Thanks

Iain

> sessionInfo()
R version 2.7.2 (2008-08-25) 
i386-apple-darwin8.11.1 

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

loaded via a namespace (and not attached):
[1] XML_1.96-0      cluster_1.11.11
> 

--- On Tue, 7/10/08, Adrian Alexa <adrian.alexa@gmail.com> wrote:
From: Adrian Alexa <adrian.alexa@gmail.com>
Subject: Re: [BioC] topGO problem
To: iaingallagher@btopenworld.com
Date: Tuesday, 7 October, 2008, 9:36 AM

Hi Iain,

try this line:

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

You need to specify the name of the parameters for the constructor of
a topGOdata. In your case, you forgot to match the annotFUN.gene2GO
with the annotationFun parameter.

Regards,
Adrian





On Mon, Oct 6, 2008 at 9:52 PM, Iain Gallagher
<iaingallagher@btopenworld.com> wrote:
> 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
>
>
>        [[alternative HTML version deleted]]
>
>
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