I am running gseGO function from clusterProfiler and getting an output where terms are ordered by the setSize parameter. What does this ranking mean? Are terms ordered by the sizes of the gene sets? If yes, then what is the ultimate value of such ranking? My goal is to get the most relevant terms, but I am not completely sure that such an ordering based on the setSize is actually the right one.

  • $\begingroup$ Did you read the clusterProfiler vignette and messages of the author in the support site and its own blog? $\endgroup$
    – llrs
    Apr 30, 2018 at 7:18
  • $\begingroup$ Sure, neither of them provide enough info. $\endgroup$ Apr 30, 2018 at 16:37
  • $\begingroup$ If you post the head of your output you are talking about, it could be easier to clarify the doubts $\endgroup$
    – llrs
    May 1, 2018 at 14:54

1 Answer 1


As you can see on this blog post of the author, the result is ordered by pvalue, but it can coincidentally sort by setSize. The setSize means that that term has so many genes on under that category.


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