Inconsistent results when running pathway analyses using Symbol/entrezid

[charliexbrown]

Hi,
I am using the ora package to perform Reactome and KEGG analyses. I have gene symbols so I used IdMapping to convert them to entrezid. From the conversion I lost a small amount of genes (eg 4 over 1700+ genes in my degs subset).

I performed the analyses both using symbol and entrezid, however I get totally different results. I considered that the loss of genes from the conversion was insignificant to explain these differences, so I was wondering what is the problem.

Thanks