Answers.Body: <p>Error is the estimation that can't be fitted by your parameters (in this case g). 
  The amova function in pegas package does the following: </p>
  
  <blockquote>
    <p>This function performs a hierarchical analysis of molecular variance as described in Excoffier et al.
    (1992). This implementation accepts any number of hierarchical levels</p>
  </blockquote>
  
  <p>And as per the definition of Fixation index, you need the variance in the frequency of the allele between different subpopulations, weighted by the sizes of the subpopulations, the variance of the allelic state in the total population. Which is not provided by amova. Thus you cannot compute the fixation index from amova results. </p>
  
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Answers.CreationDate: 2017-06-10T09:19:38.663Z
Answers.Text: That's what I thought. Thank you for confirming it. And thanks for the explanation for error!
Answers.UserDisplayName: Beatrice Baldi
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Answers.CreationDate: 2017-06-10T10:48:20.583Z
Answers.Text: @BeatriceBaldi if this answers your question, you can mark as solved by checking the tick at the left of the answer. This way you let others know that this problem is solved
Answers.UserDisplayName: llrs
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Answers.LastActivityDate: 2017-06-09T07:07:13.327Z
Answers.UserDisplayName: llrs
Body: <p>I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")</p>
  
  <p>I have two questions:</p>
  
  <ul>
  <li>What does "error" stand for?</li>
  <li>How do I calculate Fst? Which values do I have to use?</li>
  </ul>
  
  <p>A genind object in R is an object which contains allelic information about a set of individuals.<br>
  This is the table that I get: </p>
  
  <pre><code>Analysis of Molecular Variance
  
  Call: amova(formula = plantula.dist ~ g, nperm = 100)  
  
             SSD         MSD  df  
  g     354992.9 354992.9297   1  
  Error 310814.9    693.7834 448 
  Total 665807.9   1482.8683 449 
  
  Variance components:  
         sigma2 P.value  
  g     1574.69       0  
  Error  693.78         
  
  Variance coefficients:  
         a   
  224.9956   
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-08T12:35:38.683Z
Comments.Text: Welcome to Bioinformatics! Could you please clarify what is a geneind object? And could you provide the exact output of the table? (If you provide how you get that table that would probably be also helpful to answer you)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-08T12:59:49.413Z
Comments.Text: I tried to insert the table, though I can't quite format it right... sorry, I'm still figuring this out!
Comments.UserDisplayName: Beatrice Baldi
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-08T13:05:19.290Z
Comments.Text: By Fst are you refering to [Fixation index](https://en.wikipedia.org/wiki/Fixation_index)?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-08T13:05:48.867Z
Comments.Text: Please also indicate the non-standard packages you are using. I’m assuming `amova` comes from ‹pegas›?
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-08T13:19:34.047Z
Comments.Text: Yes @Llopis I mean fixation index, and yes Konard Rudolph, the amova I am using is from the package pegas.
  Sorry for not specifying!
Comments.UserDisplayName: Beatrice Baldi
Tags: <r>
Title: How to calculate Fst from AMOVA
ThreadText: # How to calculate Fst from AMOVA
  
  (Asked by: username_0 on 2017-06-08)
  
  I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")
  
  I have two questions:
  
  * What does "error" stand for?
  * How do I calculate Fst? Which values do I have to use?
  
  A genind object in R is an object which contains allelic information about a set of individuals.  
  This is the table that I get:
  
  ```
  Analysis of Molecular Variance
  
  Call: amova(formula = plantula.dist ~ g, nperm = 100)  
  
             SSD         MSD  df  
  g     354992.9 354992.9297   1  
  Error 310814.9    693.7834 448 
  Total 665807.9   1482.8683 449 
  
  Variance components:  
         sigma2 P.value  
  g     1574.69       0  
  Error  693.78         
  
  Variance coefficients:  
         a   
  224.9956   
  
  ```
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: Welcome to Bioinformatics! Could you please clarify what is a geneind object? And could you provide the exact output of the table? (If you provide how you get that table that would probably be also helpful to answer you)  
  > **username_0**: I tried to insert the table, though I can't quite format it right... sorry, I'm still figuring this out!  
  > **username_1**: By Fst are you refering to [Fixation index](https://en.wikipedia.org/wiki/Fixation_index)?  
  > **username_2**: Please also indicate the non-standard packages you are using. I’m assuming `amova` comes from ‹pegas›?  
  > **username_0**: Yes @Llopis I mean fixation index, and yes Konard username_2, the amova I am using is from the package pegas. Sorry for not specifying!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-06-09. Score: 1 | Accepted answer
  
  Error is the estimation that can't be fitted by your parameters (in this case g).
  The amova function in pegas package does the following:
  
  > This function performs a hierarchical analysis of molecular variance as described in Excoffier et al.
  > (1992). This implementation accepts any number of hierarchical levels
  
  And as per the definition of Fixation index, you need the variance in the frequency of the allele between different subpopulations, weighted by the sizes of the subpopulations, the variance of the allelic state in the total population. Which is not provided by amova. Thus you cannot compute the fixation index from amova results.
  
  > **Comments:**
  > **username_0**: That's what I thought. Thank you for confirming it. And thanks for the explanation for error!  
  > **username_1**: @username_0 if this answers your question, you can mark as solved by checking the tick at the left of the answer. This way you let others know that this problem is solved  
  
  ---
  
  