Answers.Body: <p>As you can see on <a href="https://guangchuangyu.github.io/2016/01/go-analysis-using-clusterprofiler/" rel="nofollow noreferrer">this blog</a> post of the author, the result is ordered by <code>pvalue</code>, but it can coincidentally sort by <code>setSize</code>. The <code>setSize</code> means that that term has so many genes on under that category. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-05-01T14:54:55.613Z
Answers.LastActivityDate: 2018-05-01T14:54:55.613Z
Answers.UserDisplayName: llrs
Body: <p>I am running <code>gseGO</code> function from <code>clusterProfiler</code> and getting an output where terms are ordered by the <code>setSize</code> 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 <code>setSize</code> is actually the right one.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-30T07:18:05.370Z
Comments.Text: Did you read the clusterProfiler vignette and messages of the author in the support site and its own blog?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-30T16:37:52.270Z
Comments.Text: Sure, neither of them provide enough info.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-05-01T14:54:41.733Z
Comments.Text: If you post the `head` of your output you are talking about, it could be easier to clarify the doubts
Comments.UserDisplayName: llrs
Tags: <r><clusterprofiler>
Title: What does the setSize ordering mean?
ThreadText: # What does the setSize ordering mean?
  
  (Asked by: username_0 on 2018-04-30)
  
  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.
  
  **Tags:** r, clusterprofiler
  
  > **Comments:**
  > **username_1**: Did you read the clusterProfiler vignette and messages of the author in the support site and its own blog?  
  > **username_0**: Sure, neither of them provide enough info.  
  > **username_1**: If you post the `head` of your output you are talking about, it could be easier to clarify the doubts  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-05-01. Score: 0 | Accepted answer
  
  As you can see on [this blog](https://guangchuangyu.github.io/2016/01/go-analysis-using-clusterprofiler/) 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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