[BioC] annFUN.gene2GO in topGO package

[Leonor Palmeira]

Thank you very much! That was it!
It now works like a charm.

Best,
Leonor.

Adrian Alexa a écrit :
> Hi Leonor,
> 
> The error is not triggered by the annFUN.gene2GO function. You get the
> mentioned  error since the MygeneList is a numerical vector and not a
> factor. You will need to transform it to a factor. The following line
> should build a topGOdata object without any error:
> 
> sampleGOdata <- new("topGOdata", ontology = "BP", allGenes =
> as.factor(MygeneList), annot = annFUN.gene2GO , gene2GO = Mygene2GO)
> 
> Please let me know if you have further problems.
> 
> Regards,
> Adrian
> 
> 
> 
> 
> 
> 
> On Mon, Aug 17, 2009 at 8:05 PM, Leonor
> Palmeira<palmeira at biomserv.univ-lyon1.fr> wrote:
>> Dear all,
>>
>> I have been trying to use the topGO package to identify over-represented GO
>> terms in a specific list of genes. The list does not come out of a
>> micro-array analysis and I have therefore tried to built a "topGOdata"
>> object through the following procedure :
>>
>> sampleGOdata <- new("topGOdata", ontology = "BP", allGenes = MygeneList,
>> annot = annFUN.gene2GO , gene2GO = Mygene2GO)
>>
>> However, I get the following error (some of it is in french, but it
>> basically says that the "annFUN.gene2GO" value is not a function and is of
>> class "NULL") :
>>
>> Erreur dans checkSlotAssignment(object, name, value) :
>>  l'affectation d'un objet de classe "NULL" n'est pas permise pour le slot
>> "geneSelectionFun" dans un objet de classe "topGOdata" ; is(value,
>> "function") ne renvoie pas 'TRUE'
>> De plus : Warning message:
>> In .local(.Object, ...) :
>>  No function to select the significant genes provided!
>>
>> Could you help me determine where this error comes from? I have no clue on
>> how to debug this...
>>
>> Here is a little more information on the objects used to build the
>> "topGOdata" if it can help:
>>
>> * "MygeneList" is a vector which looks like this:
>>
>>> geneList2[100:110]
>>  2DMA_HUMAN  2DMB_HUMAN  2DOA_HUMAN  2DOB_HUMAN  2DRA_HUMAN 3BHS1_HUMAN
>>          0           0           0           0           0           0
>> 3BHS2_HUMAN 3BHS7_HUMAN  3BP1_HUMAN  3BP2_HUMAN  3BP5_HUMAN
>>          0           1           0           0           0
>>
>> The 1s are for the list of genes I'm interested in, the 0s are for all the
>> other genes.
>>
>> * "MygeneList", it is a list which looks like this:
>>
>>> str(gene2GO[1:3])
>> List of 3
>>  $ NCTR3_HUMAN: chr [1:22] "GO:0045840" "GO:0009612" "GO:0006915"
>> "GO:0050806" ...
>>  $ AP3B1_HUMAN: chr [1:14] "GO:0007596" "GO:0006622" "GO:0051138"
>> "GO:0048007" ...
>>  $ AP3D1_HUMAN: chr [1:12] "GO:0048007" "GO:0051138" "GO:0019882"
>> "GO:0005515" ...
>>
>> Thank you very much in advance
>> Best,
>> Leonor.
>>
>> --
>> Leonor PALMEIRA, PhD.
>> Laboratoire de Biométrie et Biologie Évolutive
>> UMR CNRS 5558
>> UCB Lyon 1  - Bât. Grégor Mendel
>> 43, boulevard du 11 novembre 1918
>> 69622 VILLEURBANNE Cedex
>> tel : 04 72 43 28 26
>> http://lbbe.univ-lyon1.fr/-Palmeira-Leonor-.html?lang=en
>>
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>>
> 
> 
> 



-- 
Leonor PALMEIRA, PhD.
Laboratoire de Biométrie et Biologie Évolutive
UMR CNRS 5558
UCB Lyon 1  - Bât. Grégor Mendel
43, boulevard du 11 novembre 1918
69622 VILLEURBANNE Cedex
tel : 04 72 43 28 26
http://lbbe.univ-lyon1.fr/-Palmeira-Leonor-.html?lang=en