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Martin Olivier ▴ 70@martin-olivier-404
Last seen 8.1 years ago
Dear all, First, I would like to thank S. Falcon, J.W. MacDonald and J. Zhang for their help on my previous questions. I want to use the function hyperGTest on arabidopsis data, but it seems that there is a little bug in this function. This is an example that gives me an error message (hereafter, allegenes is a vector of selected genes) genesel<-c("AT1G55530", "AT5G19770" ,"AT4G10840") hyperparams<-new("GOHyperGParams",geneIds=genesel,universeGeneIds=allg enes, annotation="ath1121501",ontology="BP",pvalueCutoff=0.01,conditional=F, testDirection="over") Then if I execute the command hyperGTest(hyperparams) I obtain the error message: Erreur dans order(na.last, decreasing, ...) : l'argument 1 n'est pas un vecteur (argument 1 is not a vector) I supposed that the error comes from the fact there is no GO term in the category BP for my three genes...I tried to make some filters in such cases, but without success.... The different versions I use are : R version 2.4.0 ath1121501' version 1.14.0 GOstats' version 2.0.2 GO version 1.14.0 Thanks for your help, Olivier.