[BioC] topGO w/custom annotation

[James MacDonald]

What happens if you do

annFUN.GO2genes(GO2genes = myGO2genes)?

I don't think you need Entrez Gene IDs for topGO. What I don't 
understand is the weird mappings you are getting below.

Best,

Jim

BTW, have you emailed Adrian Alexa directly? Not sure how closely he 
follows BioC help.

Sebastien Gerega wrote:
> 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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>>
> 

-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623