# How to find DE genes between different datasets?

**URL:** <https://discourse.scverse.org/t/how-to-find-de-genes-between-different-datasets/2288>\
**Category:** scanpy\
**Tags:** integration\
**Created:** [May 20, 2024, 7:20pm UTC](https://discourse.scverse.org/t/how-to-find-de-genes-between-different-datasets/2288 "2024-05-20T19:20:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![MattC7222022](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/mattc7222022/32/1055_2.png) [@MattC7222022](https://discourse.scverse.org/u/MattC7222022)\
**Post date:** [May 20, 2024, 7:20pm UTC](https://discourse.scverse.org/t/how-to-find-de-genes-between-different-datasets/2288/1 "2024-05-20T19:20:50Z")

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Hi,  
I was wondering how you would compare different batches of scRNA-seq data with different celltypes, and get a DE gene list.

I’ve looked through the forums and found a few similar questions but nothing exact for scanpy. I’m just a bit confused because I heard you can’t run DE on batch-integrated data.

Thanks so much!

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<div class="post-metadata">

**Author:** ![emdann](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/emdann/32/254_2.png) [@emdann](https://discourse.scverse.org/u/emdann)\
**Post date:** [May 22, 2024, 9:59pm UTC](https://discourse.scverse.org/t/how-to-find-de-genes-between-different-datasets/2288/2 "2024-05-22T21:59:31Z")

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For a primer on differential expression analysis and multi-condition analysis and code examples, I would check out the “Dealing with conditions” chapters of the sc-best-practices book

[https://www.sc-best-practices.org/conditions/differential\_gene\_expression.html](https://www.sc-best-practices.org/conditions/differential_gene_expression.html)