[BioC] topGO and Arabidopsis data

Johannes Hanson s.j.hanson at uu.nl
Thu Dec 2 17:44:32 CET 2010

Dear All,

I am analyzing affymetrix expression data using the topGO package. 
I basically follow the script in the topGO vingette. It works fine for the CC and BP ontologies but for MF i get the following error:

> sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "MF", allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.db,affyLib = affyLib)

Building most specific GOs .....	( 1348 GO terms found. )

Build GO DAG topology ..........
 There are no adj nodes for node:  GO:0010241 
Error in switch(type, isa = 0, partof = 1, -1) : 
  EXPR must be a length 1 vector

I guess that there is something wrong in the annotation packages but honestly, I might well have misunderstood the error message. Using the examples in the topGO vingette and human annotation no errors are given. 

Thanks in advance,

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] topGO_2.2.0          SparseM_0.86         GO.db_2.4.5          graph_1.28.0         ath1121501.db_2.4.5  org.At.tair.db_2.4.6 RSQLite_0.9-3       
 [8] DBI_0.2-5            AnnotationDbi_1.12.0 ath1121501cdf_2.7.0  affy_1.28.0          Biobase_2.10.0      

loaded via a namespace (and not attached):
[1] affyio_1.18.0         grid_2.12.0           lattice_0.19-13       preprocessCore_1.12.0 tools_2.12.0 

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