Problem with universe values for GO categories in EnrichGO
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?
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Genes which do not belong to any ontology in the interrogated collection will be removed (see this answer). This will be different for each interrogated collection (e.g. Biological Processes, Cellular Components...), because they are composed of different gene sets. So you will have a different "N" for each collection.
enrichGO function has a
pool argument. You can use it to test across all the pooled collections, and this leads to the N being the same across all sets (I just checked).