Wolfgang,

thanks!
As you suggested, here is a full script, followed by the error message, and
then the sessionInfo().

Best regards,

Dan.

library(GO.db)
library(GOstats)
library(annotate)
library(org.Rn.eg.db)
library("Rgraphviz")
library("RBGL")
library("graph")
library("RColorBrewer")
library("geneplotter")
library("RbcBook1")

# Just some dummy genes to play with
bkg=dbGetQuery(org.Rn.eg_dbconn(), "SELECT * from genes")
bkg=bkg$gene_id
test=bkg[1:100]

params <- new("GOHyperGParams", geneIds = test,
universeGeneIds = bkg,annotation="org.Rn.eg.db",
conditional = FALSE, categoryName="GO", ontology="CC")

x=hyperGTest(params)

y=termGraphs(x,use.terms=TRUE , pvalue=.01)

plotGOTermGraph(y,x, node.colors=c(sig="white",not="blue"),
node.shape="circle", add.counts=FALSE)


Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "nodes", for signature
"list"



> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-apple-darwin8.10.1

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

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

other attached packages:
 [1] RbcBook1_1.8.0      geneplotter_1.18.0
 [3] lattice_0.17-8      RColorBrewer_1.0-2
 [5] Rgraphviz_1.18.1    org.Rn.eg.db_2.2.0
 [7] GOstats_2.6.0       Category_2.6.0
 [9] genefilter_1.20.0   survival_2.34-1
[11] RBGL_1.16.0         annotate_1.18.0
[13] xtable_1.5-2        graph_1.18.1
[15] GO.db_2.2.0         AnnotationDbi_1.2.2
[17] RSQLite_0.6-9       DBI_0.2-4
[19] Biobase_2.0.1

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22 cluster_1.11.11
>


On Thu, Sep 4, 2008 at 11:17 AM, Wolfgang Huber <huber@ebi.ac.uk> wrote:

>
> Dear Daniel
>
> thank you for your feedback! Would it be possible to
>
> (i) send a code example that we can reproduce (i.e. where the variables
> "test" and "universe" are defined)?
>
> (ii) send the output of sessionInfo() after running the example?
>
>  Best wishes
>        Wolfgang
>
> --
> ----------------------------------------------------
> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>
>
>
> daniel jupiter wrote:
>
>> Hi all,
>>
>> undoubtedly this is a silly question.
>> After struggling for quite some time, I think I've been able to do
>> hypergerometric tests for GO enrichment using hyperGTest.
>> The documentation is a bit thin, but it's eventually become clear.
>> The next step is to draw the DAG, with significant genes highlighted, and
>> term names replacing GO IDs.
>> A wrinkle: I am just interested in a particular set of genes, relative to
>> a
>> universe - there is no array, no annotation involved.
>>
>> In any case, here is my code.
>>
>> params <- new("GOHyperGParams", geneIds = test,
>> universeGeneIds = universe,annotation="org.Rn.eg.db",
>> conditional = FALSE, categoryName="GO", ontology="CC", pvalueCutoff=.01)
>>
>> x=hyperGTest(params)
>>
>> y=termGraphs(x,use.terms=TRUE , pvalue=.01)
>>
>> plotGOTermGraph(y,x, node.colors=c(sig="white",not="blue"),
>> node.shape="circle", add.counts=FALSE)
>>
>> I am returned the following error:
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "nodes", for signature
>> "list"
>>
>> Am I doing something obviously wrong?
>>
>> Any help is greatly appreciated.
>>
>> Thanks
>>
>> Dan Jupiter.
>>
>>


-- 
Daniel C. Jupiter, Ph.D.
Postdoctoral Research Associate
Department of Systems Biology and Translational Medicine
College of Medicine
Texas A&M Health Science Center
702 SW H.K. Dodgen Loop
Temple, TX 76504

979.997.2106 | Fax 254.742.7145
djupiter@tamu.edu | www.tamhsc.edu

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