Body: <p>Why differential gene expression analysis (counts) is done with multiple simple models, each with one single gene?<br />
  Why not one multivariate model with all genes simultaneously?<br />
  I mean a linear model with negative binomial distribution and using dummy variables for the genes.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-08T19:23:35.253Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-08T22:24:45.360Z
Comments.Text: Hi @skan, it is unclear what your particular biological problem is; please add detail that includes context around your biological project and problem. StackExchange does not work well with opinion-based / discussion questions. If you want to encourage a discussion, try a discussion-based site like [reddit](https://reddit.com/r/bioinformatics).
Comments.UserDisplayName: gringer
Tags: <gene-expression><modelling>
Title: Why don't we use a multivariate (all genes) model for differential expression analysis?
ThreadText: # Why don't we use a multivariate (all genes) model for differential expression analysis?
  
  (Asked by: username_0 on 2024-06-08)
  
  Why differential gene expression analysis (counts) is done with multiple simple models, each with one single gene?  
  Why not one multivariate model with all genes simultaneously?  
  I mean a linear model with negative binomial distribution and using dummy variables for the genes.
  
  **Tags:** gene-expression, modelling
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Hi @username_0, it is unclear what your particular biological problem is; please add detail that includes context around your biological project and problem. StackExchange does not work well with opinion-based / discussion questions. If you want to encourage a discussion, try a discussion-based site like [reddit](https://reddit.com/r/bioinformatics).  
  
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  ## 0 answers
  
  