Question is in the title.
GeneRatio is like M/N where M is the number of genes from your input list that match the GO term. But I don't see what is N ?
BgRatio is like A/B where B is all genes in database but I'm not sure what A corresponds to ... Is it the number of genes specific in the database of this GO term ?
Tell me if I'm wrong. Thanks.
I'm a little confused about these terms.
When 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?
Yeah I have the same problem. I don't really understand why the small n is changing then?
I am also struggling with the same problem (i.e. n and N are changing). Have you figured it out?
GeneRatio = k/n
kis the overlap between your genes-of-interest and the geneset
nis the number of all unique genes-of-interest
Mis the number of genes within each geneset
Nis the number of all unique genes across all genesets (universe)
The link is broken, but the content was archived by the Wayback Machine: https://web.archive.org/web/20171111072829/https://bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/enrichmentAnalysis.html#over-representation-analysis
Or better yet, the same info at the clusterProfiler book: http://yulab-smu.top/clusterProfiler-book/chapter2.html#over-representation-analysis