Entering edit mode
5.9 years ago
studyfranco
•
0
Hello,
I would like perform a GOTerm analysis with my rna-seq data. I have search lot of tool in R. The tool I tested are topGO. But the problem are I don't know how perform a globaltest. In the documentation, nothing about this test. I have finish the major task, but I have a error. My code :
test.stat <- new("classicExpr", testStatistic=GOglobalTest, name="Global Test")
test <- initialize(test.stat, testStatistic=GOglobalTest, exprDat=Lfc, name="Global_Test")
GOdata[[ont]] <- new("topGOdata", ontology=ont, allGenes=inputGeneList,
annot=annFUN.gene2GO, gene2GO=geneID2GO[[ont]], nodeSize=nodeSize)
resultGlobal <- getSigGroups(GOdata[["BP"]], test)
I obtain this error :
-- Classic Algorithm --
the algorithm is scoring 8990 nontrivial nodes
parameters:
test statistic: Global_Test
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
objet 'globaltest' introuvable
Have you an idea ? Or do you suggest me a another software ?
Have a nice day !