[BioC] Bug in topGO-package [topGO_1.10.0: GenTable-function]

[Adrian Alexa]

Hi Sam,

many thanks for the bug report and for the detailed description of the
problem. I solved the bug and I just checked in the changes to the
release branch. Also the version increased to 1.10.1. I hope you will
be able to download it soon enough.

Many thanks,
Adrian




On Mon, Nov 17, 2008 at 8:05 PM, Samuel Wuest <wuests at tcd.ie> wrote:
> 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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>
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