Hi List,
I have been trying to create a topGOdata object as follows:

*GOdata <- new("topGOdata", ontology = "BP", allGenes = geneList, annot
=annFUN.gene2GO, gene2GO = gene2GO)*

where, geneList and gene2GO are as described in the topGO docs.

However, I keep getting the following error:

Building most specific GOs .....
Error in annotationFun(ontology, .Object@allGenes, ...) :
  argument "gene2GO" is missing, with no default


I would appreciate any quick help on this issue.

Below is my sessionInfo:

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-redhat-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] topGO_2.2.0          SparseM_0.89         GO.db_2.4.5
[4] RSQLite_0.9-4        DBI_0.2-5            AnnotationDbi_1.12.0
[7] Biobase_2.10.0       graph_1.28.0         biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] grid_2.12.1     lattice_0.19-13 RCurl_1.5-0     tools_2.12.1
[5] XML_3.2-0




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