# How to use totalVI denoised protein measurements

**URL:** <https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850>\
**Category:** scvi-tools\
**Tags:** totalvi\
**Created:** [November 6, 2025, 5:12pm UTC](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850 "2025-11-06T17:12:16Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Zoe](https://avatars.discourse-cdn.com/v4/letter/z/a4c791/32.png) [@Zoe](https://discourse.scverse.org/u/Zoe)\
**Post date:** [November 6, 2025, 5:12pm UTC](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850/1 "2025-11-06T17:12:16Z")

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Hi! I have a sort of theoretical question about the totalVI denoised protein measurements. From the paper, it seems like for the RNA modality, there is a specific library size-based scaling factor, but it doesn’t seem like there’s something equivalent for the protein modality in the model. I was wondering if the resulting denoised protein measurements take some metric of per cell library size into account, or if they should be treated more like raw counts and if I should normalize them by some size factor?

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**Author:** ![ori-kron-wis](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ori-kron-wis/32/1099_2.png) [@ori-kron-wis](https://discourse.scverse.org/u/ori-kron-wis)\
**Post date:** [November 9, 2025, 12:58pm UTC](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850/2 "2025-11-09T12:58:56Z")

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There’s no protein scaling library size analogous to RNA, as normalization is learned internally, by tuning a mixture factor of the foreground and background proteins, per cell, in the latent space.  
You should not apply additional size factor normalization then.