Answers.Body: <p>Set <code>numberEff = True</code></p>
  <pre><code>MRcoefs(fit, coef = 2, group = 3, number = 143, eff = 5.5, numberEff = True) 
  </code></pre>
  <p>I suspect you've got the quantile value set, hence it will throw an error above 1.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-22T02:27:57.617Z
Answers.LastActivityDate: 2023-08-22T13:27:35.093Z
Answers.LastEditDate: 2023-08-22T13:27:35.093Z
Answers.UserDisplayName: M__
Body: <p>Cross-posted on biostars: <a href="https://www.biostars.org/p/9572744/" rel="nofollow noreferrer">https://www.biostars.org/p/9572744/</a></p>
  <p>I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R for calculating differentially expressed OTUs between two condition:
  my code looks like:</p>
  <pre><code>MRcoefs(fit, coef = 2, group = 3, number = 143, eff = 5.5) 
  </code></pre>
  <p>Here I am setting the eff argument to 5.5 because I have calculated the effectiv_size using this code:</p>
  <pre><code>Effective_size(fit) 
  </code></pre>
  <p>which result in table of effective size for each feature (OTU), and then I got the mean of these</p>
  <pre><code>mean(Effective_size(fit))
  </code></pre>
  <p>which was 5.5
  When I run this, it produced an error:
  prop outside [0,1], I understand it should be between 0-1, but why ? is not that number in eff is the mean that I calculated which bring 5.5 ?
  Also when I tried to run it with .5 as the document suggested as below :</p>
  <pre><code>MRcoefs(fit, coef = 2, group = 3, number = 143, eff = .5) 
  </code></pre>
  <p>it run nicely, no error , but it produced the same OTUs as when I did not include eff, I was expecting that some OTUs will be removed as they were below this threshold</p>
  <p>Could you please help me ?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-20T12:32:11.690Z
Comments.Text: Hi @MohamedSamir, firstly please put your code into coding blocks. Secondly, the package you are using is **Metagenomeseq** but the tag is **16S**. These are two different approaches, could you please clarify which you are using?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-21T16:05:34.823Z
Comments.Text: Thanks for your advice. I mean Metagenomeseq which is used for analysing 16S microbiome data. I mean MetagenomeSeq package
Comments.UserDisplayName: Mohamed Samir
Tags: <r><microbial-genomics><16rrna><microbiome>
Title: Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
ThreadText: # Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
  
  (Asked by: username_0 on 2023-08-20)
  
  Cross-posted on biostars: <https://www.biostars.org/p/9572744/>
  
  I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R for calculating differentially expressed OTUs between two condition:
  my code looks like:
  
  ```
  MRcoefs(fit, coef = 2, group = 3, number = 143, eff = 5.5) 
  
  ```
  
  Here I am setting the eff argument to 5.5 because I have calculated the effectiv\_size using this code:
  
  ```
  Effective_size(fit) 
  
  ```
  
  which result in table of effective size for each feature (OTU), and then I got the mean of these
  
  ```
  mean(Effective_size(fit))
  
  ```
  
  which was 5.5
  When I run this, it produced an error:
  prop outside [0,1], I understand it should be between 0-1, but why ? is not that number in eff is the mean that I calculated which bring 5.5 ?
  Also when I tried to run it with .5 as the document suggested as below :
  
  ```
  MRcoefs(fit, coef = 2, group = 3, number = 143, eff = .5) 
  
  ```
  
  it run nicely, no error , but it produced the same OTUs as when I did not include eff, I was expecting that some OTUs will be removed as they were below this threshold
  
  Could you please help me ?
  
  **Tags:** r, microbial-genomics, 16rrna, microbiome
  
  > **Comments:**
  > **username_1**: Hi @username_0, firstly please put your code into coding blocks. Secondly, the package you are using is **Metagenomeseq** but the tag is **16S**. These are two different approaches, could you please clarify which you are using?  
  > **username_0**: Thanks for your advice. I mean Metagenomeseq which is used for analysing 16S microbiome data. I mean MetagenomeSeq package  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-08-22. Score: 0
  
  Set `numberEff = True`
  
  ```
  MRcoefs(fit, coef = 2, group = 3, number = 143, eff = 5.5, numberEff = True) 
  
  ```
  
  I suspect you've got the quantile value set, hence it will throw an error above 1.
  
  
  ---
  
  