Body: <p>I have a binary matrix with individuals as row names, and gene name as column name.
  So, if the gene is present in an individual, we have 1, otherwise 0.</p>
  <p>I would like to cluster individuals based on the gene presence/absence pattern.</p>
  <p>Is it right to perform an MCA? Or a logistic PCA is needed?</p>
  <p>Thanks,
  Marco</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-14T14:41:42.877Z
Comments.Text: Would you consider hierarchical clustering, i.e. making a tree? However you need to present a test data set and I could give you the tree with an explanation. PCA is okay, but trees have advantages, for reasons I could explain.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-22T11:26:11.843Z
Comments.Text: I believe the answers to your question are here:
  https://help.ezbiocloud.net/gene-presenceabsence-analysis/
  https://www.biostars.org/p/66355/
Comments.UserDisplayName: Avamys
Tags: <r><clustering><pca>
Title: Clustering individuals by gene presence/absence
ThreadText: # Clustering individuals by gene presence/absence
  
  (Asked by: username_0 on 2022-10-14)
  
  I have a binary matrix with individuals as row names, and gene name as column name.
  So, if the gene is present in an individual, we have 1, otherwise 0.
  
  I would like to cluster individuals based on the gene presence/absence pattern.
  
  Is it right to perform an MCA? Or a logistic PCA is needed?
  
  Thanks,
  username_0
  
  **Tags:** r, clustering, pca
  
  > **Comments:**
  > **username_1**: Would you consider hierarchical clustering, i.e. making a tree? However you need to present a test data set and I could give you the tree with an explanation. PCA is okay, but trees have advantages, for reasons I could explain.  
  > **username_2**: I believe the answers to your question are here: https://help.ezbiocloud.net/gene-presenceabsence-analysis/ https://www.biostars.org/p/66355/  
  
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  ## 0 answers
  
  