Dear BioC community,
I have an ExpressionSet object called
eset and a list of DE genes called
deGenes, for which I want to make a GSEA.
Then I create a list of gene sets according to the ontology "molecular function".
GOobj <- annFUN.org(whichOnto = 'MF', feasibleGenes = featureNames(eset), mapping = annotation(eset),ID = 'entrez')
Next I want to make a gene set enrichment analysis, but I do not really know if this is the proper way:
r <- romer(y = exprs(eset), index = ids2indices(GOobj, deGenes), design=design, contrast=2, nrot=99)
romer function usually employed when you have a list of DE genes or am I using a wrong method?