I was running clusterprofiler in order to see enriched pathways/modules using the KEGG database. One thing I noticed after running everything and looking at my final data output with the GeneRatio and BgRatio is that the denominator of my GeneRatio is not always the same for all pathways/modules.
Menaquinone biosynthesis, modified futalosine pathway **25/7645** 251/198201 Multidrug resistance, efflux pump MexJK-OprM **25/7645** 282/198201 C10-C20 isoprenoid biosynthesis, plants **31/7645** 412/198201 Photosystem II **108/4163** 326/198201 Rebeccamycin biosynthesis, tryptophan => rebeccamycin **48/4163** 146/198201 Pyrrolnitrin biosynthesis, tryptophan => pyrrolnitrin **48/4163** 147/198201
Where the first ratio is the GeneRatio and the second ratio is the BgRatio. The BgRatio all have a denominator of 198201 which is to be expected. But my denominator changes for the GeneRatio (ex some are 7645, some are 4163...)
Anyone know why this is occurring and how to fix it? Thanks!