[BioC] topGO w/custom annotation

[Sebastien Gerega]

Hi,
actually after attempting with what I thoguht were the correct 
parameters I obtained the following error:

Building most specific GOs .....Error in annotationFun(ontology, 
.Object at allGenes, ...) :
  unused argument(s) (GO2genes = list("162.m02116" = 2403, "162.m02150" 
= 2403, "162.m02156" = c(1133, 2157, 9), "162.m02171" = 1199, 
"162.m02176" = c(2157, 1133, 9), "162.m02195" = 9, "162.m02197" = 
c(1199, 2403), "162.m02200" = c(1501, 1114, 3855, 1161, 1156, 3390, 
1195), "162.m02222" = c(208, 409, 1185), "162.m02236" = c(410, 8, 1217, 
3569), "162.m02241" = c(1133, 9, 2157), "162.m02255" = c(277, 1133), 
"162.m02262" = c(1561, 2283), "162.m02279" = c(392, 1156), "162.m02281" 
= c(1301, 1143, 1302, 1297), "162.m02286" = 2403,

Perhaps this is to do with the annFUN.gene2GO function I used. I am not 
sure how to alter the function (if necessary) for my gened IDs. Do the 
gene IDs have to ben Entrez IDs or does that not matter?
thanks,
Sebastien

James W. MacDonald wrote:
> Hi Sebasien,
>
> Sebastien Gerega wrote:
>> Hi,
>> I would like to identify overrepresented GO in my dataset using the 
>> topGO package.
>> I am working with a C. neoformans oligo array and have the GO 
>> annotation in a list with the following format:
>>
>> $`162.m02116`
>> [1] GO:0009536
>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
>>
>> $`162.m02150`
>> [1] GO:0009536
>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
>>
>> $`162.m02156`
>> [1] GO:0005554 GO:0008372 GO:0000004
>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
>>
>> How do I go about creating the GOdata object?
>>
>> GOdata = new("topGOdata",
>>            ontology = "MF",
>>            allGenes = selectedList,
>>            annot = annFUN.GO2genes,  ## the new annotation function
>>            GO2genes = myGO2genes)    ## the GO to gene ID's dataset
>>
>> Specifically what do I use for the annotation function? It is unclear 
>> to me how to write this aspect.
>
> The documentation is a bit unclear, but I believe you have things set 
> up correctly. I assume you have done the rest of the analysis and had 
> no errors?
>
> Best,
>
> Jim
>
>
>> Am I correct in understanding that I supply my list as the final 
>> argument?
>> thanks,
>> Sebastien
>>
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>