Body: <p>I have an enhancer list and I would like to see how it overlaps with histone lists from different cell types (different sizes) significantly. I would like to use a contingency table for testing but not sure which format: </p>
  
  <p>Should I use 2xk format</p>
  
  <pre><code>                         Enhancer overlap       Enhancer not overlap
  -Histone Cell Type 1             n                       n  
  -Histone Cell Type 2             n                       n  
  -Histone Cell Type 3             n                       n  
  </code></pre>
  
  <p>or individual 2x2 formats</p>
  
  <pre><code>                                  Enhancer overlap      Enhancer not overlap
  -Histone Cell Type 1 present           n                         n  
  -Histone Cell Type 1 absent            n                         n  
  
                                   Enhancer overlap      Enhancer not overlap
  -Histone Cell Type 2 present           n                         n  
  -Histone Cell Type 2 absent            n                         n  
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-08T15:10:42.813Z
Comments.Text: What do you exactly want to test? Maybe consider [edit] your question and clarifying the goal of this analysis.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-08T17:07:47.083Z
Comments.Text: the 2x2 is ok, you can test every histone (cell type) individually.... just control for multiple testing after
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-10T00:50:59.403Z
Comments.Text: I think 2x2 is the easiest way. May be you are going to use fisher's exact test? Many tests that are designed for 2x2 cannot be applied to 2xk.
Comments.UserDisplayName: Phoenix Mu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-17T22:08:58.553Z
Comments.Text: Some people would say that both schemes are inappropriate. The individual 2x2s are testing a slightly weird null, and the 2xk might be underpowered. If you're worried about this, I'd consider looking into multivariate categorical data analysis: https://journal.r-project.org/archive/2018/RJ-2018-015/RJ-2018-015.pdf. Contingency tables are still nice for looking at your data with human eyes, of course- for this purpose 2xk is more informative.
Comments.UserDisplayName: Maximilian Press
Tags: <genomefeatures>
Title: 2x2 contingency for genomic feature enrichment
ThreadText: # 2x2 contingency for genomic feature enrichment
  
  (Asked by: username_0 on 2020-05-08)
  
  I have an enhancer list and I would like to see how it overlaps with histone lists from different cell types (different sizes) significantly. I would like to use a contingency table for testing but not sure which format:
  
  Should I use 2xk format
  
  ```
                           Enhancer overlap       Enhancer not overlap
  -Histone Cell Type 1             n                       n  
  -Histone Cell Type 2             n                       n  
  -Histone Cell Type 3             n                       n  
  
  ```
  
  or individual 2x2 formats
  
  ```
                                    Enhancer overlap      Enhancer not overlap
  -Histone Cell Type 1 present           n                         n  
  -Histone Cell Type 1 absent            n                         n  
  
                                   Enhancer overlap      Enhancer not overlap
  -Histone Cell Type 2 present           n                         n  
  -Histone Cell Type 2 absent            n                         n  
  
  ```
  
  **Tags:** genomefeatures
  
  > **Comments:**
  > **username_1**: What do you exactly want to test? Maybe consider [edit] your question and clarifying the goal of this analysis.  
  > **username_2**: the 2x2 is ok, you can test every histone (cell type) individually.... just control for multiple testing after  
  > **username_3**: I think 2x2 is the easiest way. May be you are going to use fisher's exact test? Many tests that are designed for 2x2 cannot be applied to 2xk.  
  > **username_4**: Some people would say that both schemes are inappropriate. The individual 2x2s are testing a slightly weird null, and the 2xk might be underpowered. If you're worried about this, I'd consider looking into multivariate categorical data analysis: https://journal.r-project.org/archive/2018/RJ-2018-015/RJ-2018-015.pdf. Contingency tables are still nice for looking at your data with human eyes, of course- for this purpose 2xk is more informative.  
  
  ---
  
  ## 0 answers
  
  