[BioC] topGO problem

[James W. MacDonald]

Hi Iain,

Iain Gallagher 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)
> Â  go_biological_process_id ensembl_transcript_id
> 1Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0007264Â Â Â Â Â Â  ENST00000000233
> 2Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0015031Â Â Â Â Â Â  ENST00000000233
> 3Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0016192Â Â Â Â Â Â  ENST00000000233
> 4Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0006886Â Â Â Â Â Â  ENST00000000233
> 5Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0006810Â Â Â Â Â Â  ENST00000000412
> 6Â Â Â Â Â Â Â Â Â Â Â Â Â Â  GO:0006898Â Â Â Â Â Â  ENST00000000412

I certainly hope this isn't how it looks for you!

> 
> and created a list object for feeding to topGO
> 
> 
> 
> e.g.
> 
>> test1<-unstack(bio_process_go)
>> str(test1)
> List of 13847
> Â $ ENST00000000233: chr [1:4] "GO:0007264" "GO:0015031" "GO:0016192" "GO:0006886"
> Â $ ENST00000000412: chr [1:4] "GO:0006810" "GO:0006898" "GO:0008333" "GO:0015761"
> Â $ ENST00000000442: chr [1:2] "GO:0006350" "GO:0006355"
> Â $ 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)
> Â Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
> Â - 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, ...) : 
> Â  argument "annotationFun" is missing, with no default
> 
> Can anyone advise on where I'm going wrong?

I think the problem occurs because you are not naming all your 
arguments, and hence are assuming you got the placement of the 'annot' 
argument correct.

Try adding an annot = annotFUN.gene2GO to your call to new() and see if 
that helps.

Best,

Jim


> 
> 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:
> Â [1] topGO_1.8.1Â Â Â Â Â Â Â Â  SparseM_0.78Â Â Â Â Â Â Â  GO.db_2.2.0Â Â Â Â Â Â Â Â  AnnotationDbi_1.2.0
> Â [5] RSQLite_0.6-8Â Â Â Â Â Â  DBI_0.2-4Â Â Â Â Â Â Â Â Â Â  Biobase_2.0.0Â Â Â Â Â Â  graph_1.18.1Â Â Â Â Â Â  
> Â [9] biomaRt_1.14.1Â Â Â Â Â  RCurl_0.9-4Â Â Â Â Â Â Â  
> 
> loaded via a namespace (and not attached):
> [1] XML_1.96-0Â Â Â Â Â  cluster_1.11.10
> 
> 
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> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662