# Error in scvi.model.TOTALVI.setup\_anndata when loading protein-only data

**URL:** <https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697>\
**Category:** scvi-tools\
**Tags:** totalvi\
**Created:** [August 22, 2022, 8:19pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697 "2022-08-22T20:19:13Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![JohnMCMa](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/johnmcma/32/347_2.png) [@JohnMCMa](https://discourse.scverse.org/u/JohnMCMa)\
**Post date:** [August 22, 2022, 8:19pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/1 "2022-08-22T20:19:13Z")

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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-tools 1.2.X or 1.4.X.

However, the following code generates an error:

```auto
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import plotnine as p9
import scvi
import scanpy as sc
import scipy.io

sc.set_figure_params(figsize=(4, 4), color_map='cividis')
scvi.settings.seed = int(20021208)
np.random.seed(20021208)

adata = sc.read_h5ad(save_path_1+'/Hybridization_ann_single.h5')SCITO_scvi_ann = scvi.data.organize_cite_seq_10x(adata)
adata.layers["counts"] = adata.X.copy()
sc.pp.normalize_total(adata, target_sum=1e4)
adata.raw = adata
scvi.model.TOTALVI.setup_anndata(
    adata,
    protein_expression_obsm_key = 'protein_expression',
    batch_key='assignment',
    layer='counts')

```

And the full error traceback is as follows:

```auto
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-42-769f92bccbda> in <module>
      3 protein_expression_obsm_key = 'protein_expression',
      4 batch_key='assignment',
----> 5 layer='counts')

5 frames
/usr/local/lib/python3.7/dist-packages/scvi/model/_totalvi.py in setup_anndata(cls, adata, protein_expression_obsm_key, protein_names_uns_key, batch_key, layer, size_factor_key, categorical_covariate_keys, continuous_covariate_keys, **kwargs)
   1246 fields=anndata_fields, setup_method_args=setup_method_args
   1247 )
-> 1248 adata_manager.register_fields(adata, **kwargs)
   1249 cls.register_manager(adata_manager)
   1250 

/usr/local/lib/python3.7/dist-packages/scvi/data/_manager.py in register_fields(self, adata, source_registry, **transfer_kwargs)
    175 field_registry[
    176 _constants._STATE_REGISTRY_KEY
--> 177 ] = field.register_field(adata)
    178 
    179 # Compute and set summary stats for the given field.

/usr/local/lib/python3.7/dist-packages/scvi/data/fields/_layer_field.py in register_field(self, adata)
     94 
     95 def register_field(self, adata: AnnData) -> dict:
---> 96 super().register_field(adata)
     97 if self.correct_data_format:
     98 _verify_and_correct_data_format(adata, self.attr_name, self.attr_key)

/usr/local/lib/python3.7/dist-packages/scvi/data/fields/_base_field.py in register_field(self, adata)
     65 stored directly on the AnnData/MuData object.
     66 """
---> 67 self.validate_field(adata)
     68 return dict()
     69 

/usr/local/lib/python3.7/dist-packages/scvi/data/fields/_layer_field.py in validate_field(self, adata)
     84 x = self.get_field_data(adata)
     85 
---> 86 if self.is_count_data and not _check_nonnegative_integers(x):
     87 logger_data_loc = (
     88 "adata.X" if self.attr_key is None else f"adata.layers[{self.attr_key}]"

/usr/local/lib/python3.7/dist-packages/scvi/data/_utils.py in _check_nonnegative_integers(data, n_to_check)
    204 raise TypeError("data type not understood")
    205 
--> 206 inds = np.random.choice(len(data), size=(n_to_check,))
    207 check = jax.device_put(data.flat[inds], device=jax.devices("cpu")[0])
    208 negative, non_integer = _is_not_count_val(check)

```

In for your reference, the structure of `adata` right before calling `setup_anndata` is as follows:

```auto
AnnData object with n_obs × n_vars = 134136 × 0
    obs: 'assignment', 'IGg_singlet', 'UMI_antibody_raw'
    var: 'gene_ids', 'feature_types'
    uns: 'random_seed', 'log1p', 'assignment_colors'
    obsm: 'X_ADT_umap', 'protein_expression'
    layers: 'counts'

```

`adata.obsm['protein_expression']` has the expected shape ( 134136 x 136 )

A brief search shows the error has to do with empty `pandas.DataFrame` objects. However, I don’t expect gene expression is processed in Pandas in any way…?

---

<div class="post-metadata">

**Author:** ![Justin\_Hong](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/justin_hong/32/85_2.png) [@Justin\_Hong](https://discourse.scverse.org/u/Justin_Hong)\
**Post date:** [August 22, 2022, 9:47pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/2 "2022-08-22T21:47:32Z")

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Hi thanks for using scvi-tools.

Your anndata appears to have `n_vars = 0` which explains why there is an empty pandas dataframe error (the data structure underlying the `.layers` object). Are you sure you have the `counts` layer formatted correctly?

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<div class="post-metadata">

**Author:** ![JohnMCMa](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/johnmcma/32/347_2.png) [@JohnMCMa](https://discourse.scverse.org/u/JohnMCMa)\
**Post date:** [August 22, 2022, 10:26pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/3 "2022-08-22T22:26:25Z")

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@Justin_Hong  
In this case, the `counts` layer is a `scipy.sparse.csr.csr_matrix` of shape `(134136, 0)`. But, still, if there’s no RNA, then `n_vars` would certain be zero…

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<div class="post-metadata">

**Author:** ![adamgayoso](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/adamgayoso/32/100_2.png) [@adamgayoso](https://discourse.scverse.org/u/adamgayoso)\
**Post date:** [August 25, 2022, 8:28pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/4 "2022-08-25T20:28:10Z")

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For protein only, I would not advise using totalVI – unless somehow you made the RNA part of the anndata one gene of like all zeros. Is that what you’re doing?

---

<div class="post-metadata">

**Author:** ![JohnMCMa](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/johnmcma/32/347_2.png) [@JohnMCMa](https://discourse.scverse.org/u/JohnMCMa)\
**Post date:** [August 25, 2022, 8:43pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/5 "2022-08-25T20:43:58Z")

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Hi @adamgayoso : What would you recommend for protein-only data?

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<div class="post-metadata">

**Author:** ![adamgayoso](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/adamgayoso/32/100_2.png) [@adamgayoso](https://discourse.scverse.org/u/adamgayoso)\
**Post date:** [August 25, 2022, 9:28pm UTC](https://discourse.scverse.org/t/error-in-scvi-model-totalvi-setup-anndata-when-loading-protein-only-data/697/6 "2022-08-25T21:28:14Z")

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We don’t have a model at the moment. I’d be curious if you tried using one fake gene with all ones as input – I don’t think it will have much if any effect.