[BioC] annFUN.gene2GO in topGO package
Leonor Palmeira
palmeira at biomserv.univ-lyon1.fr
Tue Aug 18 09:05:01 CEST 2009
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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