# Question about interpreting the DEGs associated with disease changes using MrVI

**URL:** <https://discourse.scverse.org/t/question-about-interpreting-the-degs-associated-with-disease-changes-using-mrvi/3480>\
**Category:** scvi-tools\
**Created:** [February 11, 2025, 7:25am UTC](https://discourse.scverse.org/t/question-about-interpreting-the-degs-associated-with-disease-changes-using-mrvi/3480 "2025-02-11T07:25:20Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![zitiansunsh1ne](https://avatars.discourse-cdn.com/v4/letter/z/b9e5f3/32.png) [@zitiansunsh1ne](https://discourse.scverse.org/u/zitiansunsh1ne)\
**Post date:** [February 11, 2025, 7:25am UTC](https://discourse.scverse.org/t/question-about-interpreting-the-degs-associated-with-disease-changes-using-mrvi/3480/1 "2025-02-11T07:25:20Z")

</div>

Dear the developers of MrVI,

Thank you very much for developing this amazing tool. I am confused on the output from DE analysis, and how DEGs are defined. From the manuscript, the DEG was selected based on both p-value\<0.05 and absolute log fold change\>0.5 or 1. I understand that the model estimates each gene’s log fold change in each cell, but I did not understand why each cell only has 1 p-value for each covariate. (i.e. why there is no p-value for each gene in each cell) Are you keeping the cells whose adjusted p-values with respect to the covariate of interest are \<0.05, and selecting the genes among these cells with absolute log fold change \>0.5 as DEGs of that trait? Thank you very much for your explanation.

 ![Screenshot 2025-02-10 at 11.20.08 PM](https://canada1.discourse-cdn.com/flex035/uploads/forum11/original/2X/c/c9e234ca391b39e2ee99fd34cc265d617b7f01df.png)

---

<div class="post-metadata">

**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [February 11, 2025, 7:41am UTC](https://discourse.scverse.org/t/question-about-interpreting-the-degs-associated-with-disease-changes-using-mrvi/3480/2 "2025-02-11T07:41:46Z")

</div>

Hi, pvalue and padj are p-values of the covariate specific effect sizes in z-space using a Chi2 statistic.  
pde is similar to a p-value on the gene-by-cell level (how many random samples generated an LFC above 0.5). It is not uniform under the null hypothesis of no differential expression and is therefore not a p-value but highlights the significance of a result. See lvm-DE for a deeper discussion of this aspect: [https://www.pnas.org/doi/10.1073/pnas.2209124120](https://www.pnas.org/doi/10.1073/pnas.2209124120).

---

<div class="post-metadata">

**Author:** ![zitiansunsh1ne](https://avatars.discourse-cdn.com/v4/letter/z/b9e5f3/32.png) [@zitiansunsh1ne](https://discourse.scverse.org/u/zitiansunsh1ne)\
**Post date:** [February 11, 2025, 7:46am UTC](https://discourse.scverse.org/t/question-about-interpreting-the-degs-associated-with-disease-changes-using-mrvi/3480/3 "2025-02-11T07:46:11Z")

</div>

> [@cane11](#):
>
> re p-values of the covariate specific effect sizes in z-space using a Chi2 statistic.  
> pde is similar to a p-value on the gene-by-cell level (how many random samples generated an LFC above 0.5). It is not uniform under the null hypothesis of no differential expression and is therefore not a p-value but highlights the significance of a result. See lvm-DE for a deeper discussion of this aspect: [https://www.pnas.org/doi/10.1073/pnas.2209124120](https://www.pnas.org/doi/10.1073/pnas.2209124120).

Thank you very much for your response. I am still confused about this. In the manuscript of MrVI, when the DEG is defined as “p-value\<0.05 and absolute logFC\>1”, is the p-value referring to the pde? Then with the pde, how does MrVI select the optimal pde threshold to control FDR\<0.05 and output significant DEGs, which lvm-DE takes care of? Shall I run lvm-DE after running MrVI? Thank you very much. I truly appreciate your patience.