I was reading the documentation of rWikipathways( check link below) when I think I encountered a typo.
After running GSEA() one is to distinguish which pathways are enriched for upregulated and which for downregulated genes.
The following code is a copy of the assumed typo.
gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES>1),] #pathways enriched for upregulated lung cancer genes (1) gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES<1),] #pathways enriched for downregulated lung cancer genes (2)
In code line (2): Shouldn't it be ...$NES < -1 instead of $NES < 1?
Thanks for your answers.