[BioC] annFUN.gene2GO in topGO package

[Leonor Palmeira]

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