Hi!

I have a gene set of 1500 genes from RNA seq from which I did DGE using limma+voom then over the DGE genes I already did ORA using enrichGO analyzing MF, CC and BP:

go_enrich_1 <- enrichGO(gene = genes,
              universe = names(gene_list_1),
              OrgDb = org.Hs.eg.db,
              keyType="SYMBOL",
              ont = "ALL",
              pAdjustMethod = "fdr",
              pvalueCutoff = 0.05,
              readable = TRUE)

And ORA using the Cancer Pathways like this:

C3_t2g <- msigdbr(species = "Homo sapiens", category = "C3") %>% 
dplyr::select(gs_name, gene_symbol)
em <- enricher(genes, TERM2GENE=C3_t2g)

Let's say I would like to analyze just one pathway, more precisely the Glycolisys pathway. Can I use CAMERA method to analyze just one pathway and if yes how would I do it? And if not how can I do this?

Best, Manuel

Dear Manuel,

I refered you 5 weeks ago to a workflow using camera() for GSEA analysis (How to do GSEA over limma + voom DGE ?). Did it not work for you? The camera() workflow is the same whether you have one pathway or many.

I'm a little surprised you have used ORA for the MSigDb cancer pathways, because GSEA methods like camera() are generally considered better for this purpose.

Personally, I do tend to use roast() rather than camera() if I am testing for just one pathway in isolation. However one could use camera().

Best wishes
Gordon