Body: <p>I'd like to analyze some Copy Number Variation data produced with SNP chip technologies.</p>
  
  <p>Data is provided using contingency tables, i.e. for each gene it is provided:</p>
  
  <pre><code>         Test_Positive  Test_Negative
  Cases           [0,9]+            ...
  Controls           ...            ...
  </code></pre>
  
  <p>In example, test positive may indicate detected heterozygous deletion. In each cell there will be the count of cases/controls tested positive/negative.</p>
  
  <p>Which methodologies may be used other than Fisher's exact test?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-08T10:24:38.090Z
Comments.Text: There is the hypergeometric test. But what is your end goal, to know if certain case has an association with more CNV or to know the size of the effect of said association?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-09T07:59:52.153Z
Comments.Text: Is the data format fixed? Because it already implies the test: e.g., having just "cases" and "controls" means that you aren't using any family structures, and I imagine you could have plenty of more ways to group the CNVs rather than just one positive/negative indicator per gene.
Comments.UserDisplayName: juod
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-09T20:40:15.193Z
Comments.Text: @Llopis my end goal is to define the most recurrent and significative copy number variation, intersect them with a set of known loci involved in the disease (which I have in a bedfile) and hopefully run a pathway analysis on the most recurrent or significative ones. However, I don't know if it's sound to use this kind of data for pathway analysis and which tools may be used here
Comments.UserDisplayName: gc5
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-09T20:41:45.987Z
Comments.Text: @juod yes the data is unfortunately fixed (at least by now), I have only the indication of single copy amplification/deletion for each gene, and the number of cases/controls affected.
Comments.UserDisplayName: gc5
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-13T08:12:43.883Z
Comments.Text: This might be probably answered in stats.stackexchange.com but one of the few alternatives to fisher is the hypergeometric test (but it is closely related to the Fisher's exact test). You could also do a linear model if you tidy up a bit the data. For the pathway analysis I am not sure how to map the CNV and SNP to pathways... but there was a question on the site about it
Comments.UserDisplayName: llrs
Tags: <cnv>
Title: Methodologies for CNV analysis on SNP chip data
ThreadText: # Methodologies for CNV analysis on SNP chip data
  
  (Asked by: username_0 on 2018-02-08)
  
  I'd like to analyze some Copy Number Variation data produced with SNP chip technologies.
  
  Data is provided using contingency tables, i.e. for each gene it is provided:
  
  ```
           Test_Positive  Test_Negative
  Cases           [0,9]+            ...
  Controls           ...            ...
  
  ```
  
  In example, test positive may indicate detected heterozygous deletion. In each cell there will be the count of cases/controls tested positive/negative.
  
  Which methodologies may be used other than Fisher's exact test?
  
  **Tags:** cnv
  
  > **Comments:**
  > **username_1**: There is the hypergeometric test. But what is your end goal, to know if certain case has an association with more CNV or to know the size of the effect of said association?  
  > **username_2**: Is the data format fixed? Because it already implies the test: e.g., having just "cases" and "controls" means that you aren't using any family structures, and I imagine you could have plenty of more ways to group the CNVs rather than just one positive/negative indicator per gene.  
  > **username_0**: @Llopis my end goal is to define the most recurrent and significative copy number variation, intersect them with a set of known loci involved in the disease (which I have in a bedfile) and hopefully run a pathway analysis on the most recurrent or significative ones. However, I don't know if it's sound to use this kind of data for pathway analysis and which tools may be used here  
  > **username_0**: @username_2 yes the data is unfortunately fixed (at least by now), I have only the indication of single copy amplification/deletion for each gene, and the number of cases/controls affected.  
  > **username_1**: This might be probably answered in stats.stackexchange.com but one of the few alternatives to fisher is the hypergeometric test (but it is closely related to the Fisher's exact test). You could also do a linear model if you tidy up a bit the data. For the pathway analysis I am not sure how to map the CNV and SNP to pathways... but there was a question on the site about it  
  
  ---
  
  ## 0 answers
  
  