<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>

CC BY-SA 4.0
2020-05-08T15:10:42.813Z
What do you exactly want to test? Maybe consider [edit] your question and clarifying the goal of this analysis.
Kamil S Jaron
CC BY-SA 4.0
2020-05-08T17:07:47.083Z
the 2x2 is ok, you can test every histone (cell type) individually.... just control for multiple testing after
StupidWolf
CC BY-SA 4.0
2020-05-10T00:50:59.403Z
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.
Phoenix Mu
CC BY-SA 4.0
2020-05-17T22:08:58.553Z
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.
Maximilian Press
<genomefeatures>
2x2 contingency for genomic feature enrichment
# 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.  

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## 0 answers

