# \#totalvi

**URL:** https://discourse.scverse.org/tag/totalvi/17.md

[Latest](https://discourse.scverse.org/latest.md) · [Categories](https://discourse.scverse.org/categories.md) · [Tags](https://discourse.scverse.org/tags.md)

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## [How to use totalVI denoised protein measurements](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850)

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**Author:** [@Zoe](https://discourse.scverse.org/u/Zoe)\
**Replies:** 1\
**Last updated:** [November 9, 2025, 12:58pm UTC](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850 "2025-11-09T12:58:56Z")

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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 li…

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## [Question about get\_normalized\_expression computation](https://discourse.scverse.org/t/question-about-get-normalized-expression-computation/3842)

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**Author:** [@racng](https://discourse.scverse.org/u/racng)\
**Replies:** 3\
**Last updated:** [November 5, 2025, 8:14am UTC](https://discourse.scverse.org/t/question-about-get-normalized-expression-computation/3842 "2025-11-05T08:14:27Z")

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I have trained a TOTALVI model and I am using the get\_normalized\_expression function to get imputed values for one gene and one protein. It is using mostly CPUs (128 threads) and not the GPU (Volatile GPU-Util = 8%, 2391…

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## [Discrepancy between raw mean/non-zero proportion and LFC with model.differential\_expression](https://discourse.scverse.org/t/discrepancy-between-raw-mean-non-zero-proportion-and-lfc-with-model-differential-expression/3674)

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**Author:** [@easyeryiji](https://discourse.scverse.org/u/easyeryiji)\
**Replies:** 2\
**Last updated:** [July 10, 2025, 12:10pm UTC](https://discourse.scverse.org/t/discrepancy-between-raw-mean-non-zero-proportion-and-lfc-with-model-differential-expression/3674 "2025-07-10T12:10:37Z")

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Dear totalVI community, I’m encountering a puzzling issue while analyzing my Spatial CITE\_seq data (P\_CD8) with totalVI, and I hope someone can help me interpret the results. Here’s the key data for the gene/protein of …

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## [Workflow advice for totalVI in CITE-seq Multiplexed data](https://discourse.scverse.org/t/workflow-advice-for-totalvi-in-cite-seq-multiplexed-data/3613)

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**Author:** [@eason-sjtu](https://discourse.scverse.org/u/eason-sjtu)\
**Replies:** 3\
**Last updated:** [June 19, 2025, 5:53pm UTC](https://discourse.scverse.org/t/workflow-advice-for-totalvi-in-cite-seq-multiplexed-data/3613 "2025-06-19T17:53:52Z")

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Hi all, I’m working with CITE-seq data where 4 samples were multiplexed, stained with antibodies in a single tube, and then distributed across 4 sequencing lanes. I’d like advice on the optimal analysis workflow. Speci…

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## [Regressing out isotype controls](https://discourse.scverse.org/t/regressing-out-isotype-controls/346)

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**Author:** [@FelixTheStudent](https://discourse.scverse.org/u/FelixTheStudent)\
**Replies:** 4\
**Last updated:** [June 6, 2025, 2:44am UTC](https://discourse.scverse.org/t/regressing-out-isotype-controls/346 "2025-06-06T02:44:54Z")

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Hi scvi-tools team, thanks for the great work so far! I’d like a recommendation on whether to regress out isotype controls or not. Simply excluding them from analysis does not seem sufficient, because \> 10 actual prote…

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## [Help on MultiVI for data modality](https://discourse.scverse.org/t/help-on-multivi-for-data-modality/2134)

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**Author:** [@ksang](https://discourse.scverse.org/u/ksang)\
**Replies:** 1\
**Last updated:** [May 16, 2025, 1:33am UTC](https://discourse.scverse.org/t/help-on-multivi-for-data-modality/2134 "2025-05-16T01:33:04Z")

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In the published manuscript published in Nature Methods, it was demonstrated that MultiVI can be used on multi-omics data that include protein abundance measurements (e.g. CITE-seq). However, the tutorial on scvi-tools o…

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## [TotalVI not fully integrating CITEseq cells with GEX and missing protein values](https://discourse.scverse.org/t/totalvi-not-fully-integrating-citeseq-cells-with-gex-and-missing-protein-values/3473)

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**Author:** [@timslittle](https://discourse.scverse.org/u/timslittle)\
**Replies:** 1\
**Last updated:** [February 6, 2025, 4:38pm UTC](https://discourse.scverse.org/t/totalvi-not-fully-integrating-citeseq-cells-with-gex-and-missing-protein-values/3473 "2025-02-06T16:38:49Z")

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Hi Team, Apologies if I’m doing something wrong here! I have a CITEseq dataset in which some cells have good quality RNAseq values but poor quality ADT, so these ADT values have been removed. I tried using TotalVI to i…

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## [Impact of batch on TotalVI results](https://discourse.scverse.org/t/impact-of-batch-on-totalvi-results/3404)

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**Author:** [@JenniferF](https://discourse.scverse.org/u/JenniferF)\
**Replies:** 1\
**Last updated:** [January 5, 2025, 10:32am UTC](https://discourse.scverse.org/t/impact-of-batch-on-totalvi-results/3404 "2025-01-05T10:32:03Z")

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Good evening, thank you for maintaining TotalVI! We are applying a pre-existing model and classifier built from TotalVI to a new dataset. This new dataset includes samples across several different cancer types, patients,…

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## [\[suggestion\] what would be the appropriate pipeline to perform joint embedding of GEX and ATAC?](https://discourse.scverse.org/t/suggestion-what-would-be-the-appropriate-pipeline-to-perform-joint-embedding-of-gex-and-atac/3275)

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**Author:** [@yojetsharma](https://discourse.scverse.org/u/yojetsharma)\
**Replies:** 1\
**Last updated:** [October 17, 2024, 1:09am UTC](https://discourse.scverse.org/t/suggestion-what-would-be-the-appropriate-pipeline-to-perform-joint-embedding-of-gex-and-atac/3275 "2024-10-17T01:09:33Z")

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I have processed my snRNA of multiome using scanpy and snATAC using snapatac2. Both have been annotated as well. I would like to perform joint embedding of rna and atac but the var attributes are different and so are th…

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## [N\_samples ( refers to Monte Carlo sampling for each cell) setting in totalVI](https://discourse.scverse.org/t/n-samples-refers-to-monte-carlo-sampling-for-each-cell-setting-in-totalvi/2340)

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**Author:** [@qingjiao](https://discourse.scverse.org/u/qingjiao)\
**Replies:** 1\
**Last updated:** [June 28, 2024, 1:22am UTC](https://discourse.scverse.org/t/n-samples-refers-to-monte-carlo-sampling-for-each-cell-setting-in-totalvi/2340 "2024-06-28T01:22:39Z")

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Hi :slight\_smile: I have a question about the n\_samples ( refers to Monte Carlo sampling for each cell) setting in totalVI. In the tutorial ( CITE-seq analysis with totalVI — scvi-tools), n\_samples is set to 25 in get…

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## [Failing to import SCVI-tools modules: has AnnDatasetFromAnnData been replaced?](https://discourse.scverse.org/t/failing-to-import-scvi-tools-modules-has-anndatasetfromanndata-been-replaced/2359)

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**Author:** [@Adam](https://discourse.scverse.org/u/Adam)\
**Replies:** 2\
**Last updated:** [June 27, 2024, 7:10pm UTC](https://discourse.scverse.org/t/failing-to-import-scvi-tools-modules-has-anndatasetfromanndata-been-replaced/2359 "2024-06-27T19:10:15Z")

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Hello! I am attempting to learn how to use totalVI to analyze big CITE seq datasets after reading This paper regarding thymic development. There was an abundance of code provided, and I had hoped to work through it to re…

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## [Integration of Multiple Multiome Datasets](https://discourse.scverse.org/t/integration-of-multiple-multiome-datasets/1685)

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**Author:** [@jjuhh](https://discourse.scverse.org/u/jjuhh)\
**Replies:** 5\
**Last updated:** [March 6, 2024, 9:45pm UTC](https://discourse.scverse.org/t/integration-of-multiple-multiome-datasets/1685 "2024-03-06T21:45:43Z")

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Thank you for developing a bunch of amazing tools in the single-cell field! I encountered an issue related to the integration of multiple multiome datasets. As I understand, totalVI is specialized in CITE-seq(protein +…

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## [Questions about scib weight choice](https://discourse.scverse.org/t/questions-about-scib-weight-choice/1941)

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**Author:** [@HelloWorldLTY](https://discourse.scverse.org/u/HelloWorldLTY)\
**Replies:** 0\
**Last updated:** [December 5, 2023, 4:16am UTC](https://discourse.scverse.org/t/questions-about-scib-weight-choice/1941 "2023-12-05T04:16:37Z")

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Hi, I have a quick question about the setting of the weighted sum in scIB: I understand to assgin S\_bio with 0.6 and S\_batch as 0.4 are to ensure bio convservation is more important. However, I wonder what is the mot…

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## [Vae\_q.latent\_space\_classifer\_ not found in totalVI CITE-seq reference mapping tutorial](https://discourse.scverse.org/t/vae-q-latent-space-classifer-not-found-in-totalvi-cite-seq-reference-mapping-tutorial/1859)

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**Author:** [@JenniferF](https://discourse.scverse.org/u/JenniferF)\
**Replies:** 3\
**Last updated:** [November 20, 2023, 8:59pm UTC](https://discourse.scverse.org/t/vae-q-latent-space-classifer-not-found-in-totalvi-cite-seq-reference-mapping-tutorial/1859 "2023-11-20T20:59:42Z")

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We are following the tutorial located here to create a reference and map cell idents to a query. CITE-seq reference mapping with totalVI — scvi-tools In “Query cell type prediction”, we receive an error that vae\_q does …

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## [Multi-omics scANVI](https://discourse.scverse.org/t/multi-omics-scanvi/1879)

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**Author:** [@racng](https://discourse.scverse.org/u/racng)\
**Replies:** 1\
**Last updated:** [November 14, 2023, 7:24pm UTC](https://discourse.scverse.org/t/multi-omics-scanvi/1879 "2023-11-14T19:24:41Z")

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Is there an extension of the scANVI model that could also model protein data from CITE-seq like totalVI?

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## [RuntimeWarning: The lr scheduler dict contains the key(s)](https://discourse.scverse.org/t/runtimewarning-the-lr-scheduler-dict-contains-the-key-s/1830)

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**Author:** [@amaukisumi](https://discourse.scverse.org/u/amaukisumi)\
**Replies:** 0\
**Last updated:** [October 23, 2023, 1:55pm UTC](https://discourse.scverse.org/t/runtimewarning-the-lr-scheduler-dict-contains-the-key-s/1830 "2023-10-23T13:55:34Z")

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Hello: I recently got the following problem while analyzing CITE-Seq data with TOTALVI: RuntimeWarning: The lr scheduler dict contains the key(s) \['monitor'\], but the keys will be ignored. you need to call lr\_scheduler.…

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## [How to properly save and load a TotalVI trained model that's based on mudata?](https://discourse.scverse.org/t/how-to-properly-save-and-load-a-totalvi-trained-model-thats-based-on-mudata/1749)

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**Author:** [@hmnzo5gy](https://discourse.scverse.org/u/hmnzo5gy)\
**Replies:** 1\
**Last updated:** [September 7, 2023, 8:52pm UTC](https://discourse.scverse.org/t/how-to-properly-save-and-load-a-totalvi-trained-model-thats-based-on-mudata/1749 "2023-09-07T20:52:41Z")

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I set up the totalVI model using mudata scvi.model.TOTALVI.setup\_mudata( mdata, rna\_layer="counts", protein\_layer=None, batch\_key="batch", modalities={ "rna\_layer": "rna\_subset", "pro…

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## [TypeError when trying to set up scvi.model.TOTALVI()](https://discourse.scverse.org/t/typeerror-when-trying-to-set-up-scvi-model-totalvi/1709)

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**Author:** [@hmnzo5gy](https://discourse.scverse.org/u/hmnzo5gy)\
**Replies:** 2\
**Last updated:** [August 29, 2023, 3:57am UTC](https://discourse.scverse.org/t/typeerror-when-trying-to-set-up-scvi-model-totalvi/1709 "2023-08-29T03:57:54Z")

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When I try to set up MuData model for TotalVI using scvi.model.TOTALVI(mdata), I keep encountering “Type Error”: A sparse matrix was passed, but dense data is required. Use X.toarray() to convert to a dense numpy array. …

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## [Increase number of CPU cores for vae.train() in scvi?](https://discourse.scverse.org/t/increase-number-of-cpu-cores-for-vae-train-in-scvi/1714)

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**Author:** [@hmnzo5gy](https://discourse.scverse.org/u/hmnzo5gy)\
**Replies:** 3\
**Last updated:** [August 28, 2023, 9:03pm UTC](https://discourse.scverse.org/t/increase-number-of-cpu-cores-for-vae-train-in-scvi/1714 "2023-08-28T21:03:51Z")

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When I run vae.train(use\_gpu=False), how can I increase number of CPU cores for parallel processing?

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## [Debugging Issue for CITE-seq analysis with totalVI juytper notebook tutorial](https://discourse.scverse.org/t/debugging-issue-for-cite-seq-analysis-with-totalvi-juytper-notebook-tutorial/1516)

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**Author:** [@Bakar](https://discourse.scverse.org/u/Bakar)\
**Replies:** 6\
**Last updated:** [June 21, 2023, 6:51pm UTC](https://discourse.scverse.org/t/debugging-issue-for-cite-seq-analysis-with-totalvi-juytper-notebook-tutorial/1516 "2023-06-21T18:51:18Z")

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I am having issues addressing a error when trying to go through the CITE-seq analysis with totalVI notebook on my personal computer. An error surfaces when I try to run the following cell block: --------------------…

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## [Totalvi failing to write an h5mu objecy](https://discourse.scverse.org/t/totalvi-failing-to-write-an-h5mu-objecy/1405)

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**Author:** [@deevdevil88](https://discourse.scverse.org/u/deevdevil88)\
**Replies:** 7\
**Last updated:** [May 10, 2023, 10:15am UTC](https://discourse.scverse.org/t/totalvi-failing-to-write-an-h5mu-objecy/1405 "2023-05-10T10:15:03Z")

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Hello, I have recently been encountering an error while running totalvi. Totalvi finishes running the model fine, but errors when trying to write out the h5mu object file. …

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## [Dataset integration and analysis](https://discourse.scverse.org/t/dataset-integration-and-analysis/1342)

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**Author:** [@mdbabumiamssm](https://discourse.scverse.org/u/mdbabumiamssm)\
**Replies:** 3\
**Last updated:** [May 3, 2023, 5:33pm UTC](https://discourse.scverse.org/t/dataset-integration-and-analysis/1342 "2023-05-03T17:33:11Z")

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Hi everyone, I am working on multiple GEO datasets on a specific blood cancer. My intention is to download cell ranger processed raw data (as available) from GEO and then pre-process, integrate, and use the datasets for…

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## [totalVI, peakVI, multiVI with scRNA-seq and scATAC-seq data](https://discourse.scverse.org/t/totalvi-peakvi-multivi-with-scrna-seq-and-scatac-seq-data/296)

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**Author:** [@Z\_Huang](https://discourse.scverse.org/u/Z_Huang)\
**Replies:** 3\
**Last updated:** [March 9, 2023, 5:53pm UTC](https://discourse.scverse.org/t/totalvi-peakvi-multivi-with-scrna-seq-and-scatac-seq-data/296 "2023-03-09T17:53:07Z")

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Hi community, I am new to scvi-tools and I went through all of the tutorials. I learned peakVI consumes scATAC-seq data for DNA analysis; totalVI consumes CITE-seq data for RNA and protein analysis. Here is my question…

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## [3 sets of CITE-Seq data, how to concatenate or make single file for further analysis?](https://discourse.scverse.org/t/3-sets-of-cite-seq-data-how-to-concatenate-or-make-single-file-for-further-analysis/1116)

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**Author:** [@mdbabumiamssm](https://discourse.scverse.org/u/mdbabumiamssm)\
**Replies:** 0\
**Last updated:** [February 7, 2023, 10:17pm UTC](https://discourse.scverse.org/t/3-sets-of-cite-seq-data-how-to-concatenate-or-make-single-file-for-further-analysis/1116 "2023-02-07T22:17:02Z")

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Hi everyone , I have 3 sets of similar CITE-Seq data, i performed pre-processing individually using Muon+scanpy. Now, I want to make them as single file and perform comparative analysis. Any help ? Thanks in advance. …

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## [multiVI and totalVI modal integration question](https://discourse.scverse.org/t/multivi-and-totalvi-modal-integration-question/743)

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**Author:** [@yulijia](https://discourse.scverse.org/u/yulijia)\
**Replies:** 0\
**Last updated:** [September 15, 2022, 12:55pm UTC](https://discourse.scverse.org/t/multivi-and-totalvi-modal-integration-question/743 "2022-09-15T12:55:46Z")

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Hi, Recently, I am using scvi-tools to generate multi-modal integrated datasets. I have a question about the MULTIVI.get\_latent\_representation and TOTALVI.get\_latent\_representation function. I followed the user guide …

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## [TotalVI log normalization and non-negativity](https://discourse.scverse.org/t/totalvi-log-normalization-and-non-negativity/421)

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**Author:** [@frankligy](https://discourse.scverse.org/u/frankligy)\
**Replies:** 4\
**Last updated:** [September 11, 2022, 10:51pm UTC](https://discourse.scverse.org/t/totalvi-log-normalization-and-non-negativity/421 "2022-09-11T22:51:32Z")

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Hello, I was wondering about two questions: \[1\] Would that make sense to do log2 transformation on the denoised protein value (totalVI output)? \[2\] It looks like the totalVI output denoised protein value are all non-n…

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## [Error in scvi.model.TOTALVI.setup\_anndata when loading protein-only data](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697)

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**Author:** [@JohnMCMa](https://discourse.scverse.org/u/JohnMCMa)\
**Replies:** 5\
**Last updated:** [August 25, 2022, 9:28pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697 "2022-08-25T21:28:14Z")

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Hi, This is my first post here, so please apologize if I did something wrong. I have been using TOTALVI for protein-only CITE-seq analyses for quite a while, and I’m sure I have been able to get good results using scvi…

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## [Advice regarding complex multimodal integration/analysis strategy](https://discourse.scverse.org/t/advice-regarding-complex-multimodal-integration-analysis-strategy/647)

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**Author:** [@amagen](https://discourse.scverse.org/u/amagen)\
**Replies:** 0\
**Last updated:** [July 28, 2022, 3:19pm UTC](https://discourse.scverse.org/t/advice-regarding-complex-multimodal-integration-analysis-strategy/647 "2022-07-28T15:19:12Z")

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Hi all, I have a couple of human cancer types, each with different modalities (scRNAseq,CITEseq,MERFISH for cancer type #1 and scRNAseq,CITEseq,scATACseq,multiome for cancer type #2), some have different technology vers…

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## [The totalVI DE test; gene names](https://discourse.scverse.org/t/the-totalvi-de-test-gene-names/474)

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**Author:** [@Milcah](https://discourse.scverse.org/u/Milcah)\
**Replies:** 2\
**Last updated:** [May 24, 2022, 2:29pm UTC](https://discourse.scverse.org/t/the-totalvi-de-test-gene-names/474 "2022-05-24T14:29:23Z")

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Hello, I was using the totalVI de test with scvi tools 0.13.0. After updating to scvi tools 0.16.0 I am not able to get the gene names as the first column of the de\_df matrix. Rather, the first column is the number corr…

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## [ScArches-TotalVI reproducibility](https://discourse.scverse.org/t/scarches-totalvi-reproducibility/463)

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**Author:** [@Nusob888](https://discourse.scverse.org/u/Nusob888)\
**Replies:** 15\
**Last updated:** [May 19, 2022, 11:38am UTC](https://discourse.scverse.org/t/scarches-totalvi-reproducibility/463 "2022-05-19T11:38:00Z")

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Hi all, Having read the recent lung atlas preprint, I have realised that they implement a different approach to atlas extension than what is described in scvi-tools and scarches tutorials. In the reproducibility code t…

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