Thank you very much! That was it! It now works like a charm. Best, Leonor. Adrian Alexa a ?crit : > 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 Biom?trie et Biologie ?volutive >> UMR CNRS 5558 >> UCB Lyon 1 - B?t. Gr?gor 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- Leonor PALMEIRA, PhD. Laboratoire de Biom?trie et Biologie ?volutive UMR CNRS 5558 UCB Lyon 1 - B?t. Gr?gor 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