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Samuel Wuest
▴
330
@samuel-wuest-2821
Last seen 10.2 years ago
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
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