[BioC] TopGO 0 nontrivial nodes
Dario Strbenac
dstr7320 at uni.sydney.edu.au
Thu Jul 25 10:00:15 CEST 2013
Hello,
I don't understand why TopGO wouldn't work with gene symbols
GOdata <- new("topGOdata", ontology = GOcategory, allGenes = allGenes, annotationFun = annFUN.org, nodeSize = 10, mapping = "org.Hs.eg.db", ID = "symbol")
test <- new("classicCount", testStatistic = GOFisherTest)
testResult <- getSigGroups(GOdata, test)
Gives as a result :
-- Classic Algorithm --
the algorithm is scoring 0 nontrivial nodes
parameters:
test statistic:
Note that allGenes is
I have topGO_2.12.0 and R 3.0.1
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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