<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>

CC BY-SA 4.0
2024-06-08T19:23:35.253Z
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.
Community
CC BY-SA 4.0
2024-06-08T22:24:45.360Z
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).
gringer
<gene-expression><modelling>
Why don't we use a multivariate (all genes) model for differential expression analysis?
# 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 @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).  

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