# The output of scANVI

**URL:** <https://discourse.scverse.org/t/the-output-of-scanvi/2324>\
**Category:** scvi-tools\
**Tags:** integration, scanvi, scvi\
**Created:** [June 10, 2024, 5:38am UTC](https://discourse.scverse.org/t/the-output-of-scanvi/2324 "2024-06-10T05:38:26Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ngvananh2508](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ngvananh2508/32/708_2.png) [@ngvananh2508](https://discourse.scverse.org/u/ngvananh2508)\
**Post date:** [June 10, 2024, 5:38am UTC](https://discourse.scverse.org/t/the-output-of-scanvi/2324/1 "2024-06-10T05:38:26Z")

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Hi,  
Thank for the wonderful libraries.  
I have some questions. After doing integration, should I get model\_scanvi.get\_latent\_represention() or model\_scanvi.get\_normalized\_expression() as a new X matrix to do downstream analysis such as DGE or GSEA? When I plotted the UMAP of get\_normalized\_expression() method, the result is not really integrated in the right way.

 ![image](https://canada1.discourse-cdn.com/flex035/uploads/forum11/original/2X/2/2810431ba209a65aa1258db09a9689f5dee7b0b0.png)  
The output matrix of get\_latent\_representation() has negative values. If we should take this matrix as X of annotated data, how can we avoid these negative values (by setting some parameters of scANVI or scVI)  
Thank you so much for helping me!

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**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:** [June 19, 2024, 3:36am UTC](https://discourse.scverse.org/t/the-output-of-scanvi/2324/2 "2024-06-19T03:36:25Z")

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Responded on GitHub to the same question. In short latent representation goes into obsm and not X.

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**Author:** ![ngvananh2508](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ngvananh2508/32/708_2.png) [@ngvananh2508](https://discourse.scverse.org/u/ngvananh2508)\
**Post date:** [June 19, 2024, 4:05am UTC](https://discourse.scverse.org/t/the-output-of-scanvi/2324/3 "2024-06-19T04:05:33Z")

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Thank you so much! \<3