Dear all,

I don't know whether anyone has noticed this as well, but I think there is a
bug in the newest version of the topGO-package: the function GenTable spits
out everything correctly (as far as I can see), with the exception that the
Terms are sorted incorrectly (so the GO-ids are ok, but the Descriptions do
not fit the IDs).
Any feedback? Best wishes and thanks a million...

Sam

Please see the following code for example:
# loading the libraries
> library(topGO)
> library(hgu133plus2.db)
# generating a random list for demonstration purposes
>  All <-  ls(hgu133plus2ACCNUM)
> sigGenes <- All[1:1000]
> geneList <- factor(as.integer(All %in% sigGenes))
> names(geneList) <- All

# topGO-analysis
> GOdata <- new("topGOdata", ontology = "CC", allGenes = geneList, annot =
annFUN.db, affyLib="hgu133plus2.db")

Building most specific GOs .....    ( 717 GO terms found. )

Build GO DAG topology ..........    ( 869 GO terms and 1653 relations. )

Annotating nodes ...............    ( 32026 genes annotated to the GO terms.
)
>
> test.stat <- new("weightCount", testStatistic = GOFisherTest, name =
"Fisher test", sigRatio = "ratio", cutOff=0.01)
> resultWeight <- getSigGroups(GOdata, test.stat)

             -- Weight Algorithm --

         The algorithm is scoring 277 nontrivial nodes
         parameters:
             test statistic:  Fisher test : ratio

     Level 15:    1 nodes to be scored.

etc...

## here comes the bug: the Term column is sorted incorrectly:

> allRes <- GenTable(GOdata, weight = resultWeight,  topNodes = 5)
> allRes
       GO.ID                            Term Annotated Significant Expected
weight
1 GO:0031224                 lateral element      9657         283   214.09
2.1e-08
2 GO:0019028                    viral capsid         7           2     0.16
0.0096
3 GO:0033017           intrinsic to membrane        26           3     0.58
0.0193
4 GO:0000800               perinuclear theca        10           2     0.22
0.0196
5 GO:0033011 sarcoplasmic reticulum membrane         1           1     0.02
0.0222

# compare against:

> mget(allRes[1:3,1], GOTERM)
$`GO:0031224`
GOID: GO:0031224
Term: intrinsic to membrane
Ontology: CC
Definition: Located in a membrane such that some covalently attached portion
of the gene product, for example part of a peptide
    sequence or some other covalently attached moiety such as a GPI anchor,
spans or is embedded in one or both leaflets of the
    membrane.

$`GO:0019028`
GOID: GO:0019028
Term: viral capsid
Ontology: CC
Definition: The protein coat that surrounds the infective nucleic acid in
some virus particles. It comprises numerous regularly
    arranged subunits, or capsomeres.
Synonym: viral capsid (sensu Retroviridae)
Synonym: GO:0046728
Secondary: GO:0046728

$`GO:0033017`
GOID: GO:0033017
Term: sarcoplasmic reticulum membrane
Ontology: CC
Definition: The lipid bilayer surrounding the sarcoplasmic reticulum.



> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8

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

other attached packages:
[1] hgu133plus2.db_2.2.5 topGO_1.10.0         SparseM_0.78
GO.db_2.2.5          RSQLite_0.7-1        DBI_0.2-4
[7] AnnotationDbi_1.4.1  Biobase_2.2.0        graph_1.20.0

loaded via a namespace (and not attached):
[1] cluster_1.11.11

	[[alternative HTML version deleted]]

