I got a problem with universe values for three ontology categories.
I've used the same gene set, why do my numbers of n and N change when doing gene ontology for different categories?
For example, for the same gene list for an overrepresentation test in Biological Processes for taxis, GeneRatio is 209/3770 and BGRatio is 440/12553 but for Cellular Components for the term extracellular matrix, the Gene Ratio is 162/3963 and Bg Ratio is 339/13183. Shouldn't the n and N values stay the same in different GO categories?