[BioC] annFUN.gene2GO in topGO package

[Adrian Alexa]

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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