[BioC] new topGO results using GO.db very different from old ones using GO

[Joern Toedling]

Dear all,
I would appreciate any suggestion on the following issue. I have noticed 
a major inconsistency between new and older topGO results. For the older 
ones, topGO used the "GO" package, while it uses "GO.db" for the new 
results I can't figure out whether it is a problem with topGO only or 
whether there are some serious inconsistencies between GO and GO.db

Here is the source code I used:

library("topGO")

## load list of genes of interest

load("brainOnlyGenes.RData")

## load genereal gene-to-GO mapping and universe of genes to use in analysis:

load("mm9gene2GO.RData")

load("arrayGenesWithGO.RData")

## then the function to call topGO and to return a nice result table:

sigGOTable <- function(selGenes, GOgenes=arrayGenesWithGO, 

 gene2GO=mm9.gene2GO[arrayGenesWithGO], ontology="BP", maxP=0.001)

{

  inGenes <- factor(as.integer(GOgenes %in% selGenes))

  names(inGenes) <- GOgenes

  GOdata <- new("topGOdata", ontology=ontology, allGenes=inGenes, 

                annot=annFUN.gene2GO, gene2GO=gene2GO)

  myTestStat <- new("elimCount", testStatistic=GOFisherTest, 

                    name="Fisher test", cutOff=maxP)

  mySigGroups <- getSigGroups(GOdata, myTestStat)

  sTab <- GenTable(GOdata, mySigGroups, topNodes=length(usedGO(GOdata)))

  names(sTab)[length(sTab)] <- "p.value"

  return(subset(sTab, as.numeric(p.value) < maxP))

}#

## call it:

(brainRes <- sigGOTable(brainOnlyGenes))

# with  topGO_1.4.0  using GO_2.0.1

# this is:

#         GO.ID                  Term Annotated Significant Expected p.value
#  1 GO:0007268 synaptic transmission       136          44    24.46 3.0e-05
#  2 GO:0007610              behavior       180          54    32.38 4.4e-05
#  3 GO:0007409          axonogenesis       119          38    21.41 0.00014
#  4 GO:0006887            exocytosis        40          17     7.20 0.00026
#  5 GO:0007420     brain development       136          40    24.46 0.00066


# which kind of make sense if it somehow to annotate a list of interesting genes when investigating brain cells

## now unfortunately using all the same gene list, universe and gene-to-GO mapping, and the same function as above

##  with topGO_1.9.0  using GO.db_2.2.0, the result is:

#        GO.ID                                Term Annotated Significant Expected  p.value
# 1 GO:0007268    mitochondrial genome maintenance       137          44    24.65  3.7e-05
# 2 GO:0007610                        reproduction       180          54    32.39  4.4e-05
# 3 GO:0007409          single strand break repair       119          38    21.41  0.00014
# 4 GO:0006887     regulation of DNA recombination        40          17     7.20  0.00026
# 5 GO:0007420 regulation of mitotic recombination       136          40    24.47  0.00066


# which is obviously very, very different


Does anyone have an educated guess what is going on? Could it be a bug a 
in topGO? Or is the information in GO.db really different from the one 
in GO, and in that case which one is the right one?

Best regards,
Joern