KeyError: 'base' when running tl.rank_genes_groups

[naity2]

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the master branch of scanpy.

---

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

# Your code here
sc.tl.rank_genes_groups(adata, "origin", method="wilcoxon")

[Paste the error output produced by the above code here]
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Input In [18], in <cell line: 1>()
----> 1 sc.tl.rank_genes_groups(adata, "origin", method="wilcoxon")
      2 sc.pl.rank_genes_groups(adata, n_genes=25, sharey=False)

File ~/app/miniconda3/envs/bio/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:590, in rank_genes_groups(adata, groupby, use_raw, groups, reference, n_genes, rankby_abs, pts, key_added, copy, method, corr_method, tie_correct, layer, **kwds)
    580 adata.uns[key_added] = {}
    581 adata.uns[key_added]['params'] = dict(
    582     groupby=groupby,
    583     reference=reference,
   (...)
    587     corr_method=corr_method,
    588 )
--> 590 test_obj = _RankGenes(adata, groups_order, groupby, reference, use_raw, layer, pts)
    592 if check_nonnegative_integers(test_obj.X) and method != 'logreg':
    593     logg.warning(
    594         "It seems you use rank_genes_groups on the raw count data. "
    595         "Please logarithmize your data before calling rank_genes_groups."
    596     )

File ~/app/miniconda3/envs/bio/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:93, in _RankGenes.__init__(self, adata, groups, groupby, reference, use_raw, layer, comp_pts)
     82 def __init__(
     83     self,
     84     adata,
   (...)
     90     comp_pts=False,
     91 ):
---> 93     if 'log1p' in adata.uns_keys() and adata.uns['log1p']['base'] is not None:
     94         self.expm1_func = lambda x: np.expm1(x * np.log(adata.uns['log1p']['base']))
     95     else:

KeyError: 'base'

Versions

[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]

anndata 0.8.0
scanpy 1.9.1

Levenshtein NA
OpenSSL 21.0.0
PIL 9.1.0
adjustText NA
airr 1.3.1
appdirs 1.4.4
asttokens NA
attr 21.4.0
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
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boto3 1.21.42
botocore 1.24.42
brotli NA
bs4 4.11.1
cattr NA
certifi 2021.10.08
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cython_runtime NA
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debugpy 1.6.0
decorator 5.1.1
defusedxml 0.7.1
easydev 0.12.0
entrypoints 0.4
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gseapy 0.10.8
h5py 3.6.0
hypergeom_ufunc NA
idna 3.3
igraph 0.9.10
ipykernel 6.13.0
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joblib 1.1.0
jupyter_server 1.16.0
kiwisolver 1.4.2
leidenalg 0.8.9
llvmlite 0.38.0
lxml 4.8.0
matplotlib 3.5.1
matplotlib_inline NA
mpl_toolkits NA
natsort 8.1.0
nbinom_ufunc NA
networkx 2.8
numba 0.55.1
numpy 1.21.6
packaging 21.3
pandas 1.4.2
parasail 1.2.4
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.29
psutil 5.9.0
ptyprocess 0.7.0
pure_eval 0.2.2
pycparser 2.21
pydev_ipython NA
pydevconsole NA
pydevd 2.8.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pyexpat NA
pygments 2.11.2
pylab NA
pynndescent 0.5.6
pyparsing 3.0.8
pytoml NA
pytz 2022.1
requests 2.27.1
requests_cache 0.9.2
scipy 1.8.0
scirpy 0.10.1
seaborn 0.11.2
session_info 1.0.0
setuptools_scm NA
six 1.16.0
sklearn 1.0.2
socks 1.7.1
soupsieve 2.3.2.post1
stack_data 0.2.0
statsmodels 0.13.2
texttable 1.6.4
threadpoolctl 3.1.0
tornado 6.1
tqdm 4.62.3
tracerlib NA
traitlets 5.1.1
typing_extensions NA
umap 0.5.3
url_normalize 1.4.3
urllib3 1.26.7
wcwidt

[auesro]

Same error here...any ideas?

-----
anndata     0.8.0
scanpy      1.8.2
sinfo       0.3.1
-----
PIL                         9.0.1
PyQt5                       NA
anndata                     0.8.0
anndata2ri                  0.0.0
atomicwrites                1.4.0
autoreload                  NA
backcall                    0.2.0
backports                   NA
beta_ufunc                  NA
binom_ufunc                 NA
bs4                         4.10.0
cached_property             1.5.2
cffi                        1.15.0
chardet                     4.0.0
cloudpickle                 2.0.0
colorama                    0.4.4
cycler                      0.10.0
cython_runtime              NA
cytoolz                     0.11.2
dask                        2022.02.0
dateutil                    2.8.2
debugpy                     1.5.1
decorator                   5.1.1
defusedxml                  0.7.1
dunamai                     1.10.0
entrypoints                 0.4
fsspec                      2022.02.0
get_version                 3.5.4
h5py                        3.6.0
igraph                      0.9.9
ipykernel                   6.9.1
jedi                        0.18.1
jinja2                      3.0.3
joblib                      1.1.0
kiwisolver                  1.3.2
leidenalg                   0.8.9
llvmlite                    0.38.0
louvain                     0.7.1
markupsafe                  2.1.0
matplotlib                  3.5.1
matplotlib_inline           NA
mpl_toolkits                NA
natsort                     8.1.0
nbinom_ufunc                NA
numba                       0.55.1
numexpr                     2.8.0
numpy                       1.21.5
packaging                   21.3
pandas                      1.3.5
parso                       0.8.3
pexpect                     4.8.0
pickleshare                 0.7.5
pkg_resources               NA
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pydevd                      2.6.0
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pytz                        2021.3
pytz_deprecation_shim       NA
rpy2                        3.4.2
scanpy                      1.8.2
scipy                       1.7.3
seaborn                     0.11.2
setuptools                  59.8.0
sinfo                       0.3.1
sip                         NA
six                         1.16.0
sklearn                     1.0.2
soupsieve                   2.3.1
sphinxcontrib               NA
spyder                      5.2.2
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spydercustomize             NA
statsmodels                 0.13.2
storemagic                  NA
tables                      3.7.0
texttable                   1.6.4
threadpoolctl               3.1.0
tlz                         0.11.2
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tornado                     6.1
traitlets                   5.1.1
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yaml                        6.0
zipp                        NA
zmq                         22.3.0
-----
IPython             7.32.0
jupyter_client      7.1.2
jupyter_core        4.9.2
-----
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) [GCC 9.4.0]
Linux-5.4.0-109-generic-x86_64-with-debian-bullseye-sid
16 logical CPU cores, x86_64
-----
Session information updated at 2022-04-20 18:16

[Koncopd]

And what is in adata.uns['log1p']?

[auesro]

Its empty, there is no base key.

I just found issue #2181 which mentions the same issue and a workaround. In case @naity2 or someone else comes looking.

[naity2]

Thank you @auesro!

For now, I use the line adata.uns['log1p']["base"] = None every time after reading a h5ad file.

[brianpenghe]

adata.uns['log1p']["base"] = None

Thank you. I also had this error when calculating highly variable genes sc.pp.highly_variable_genes(Adult,batch_key='batch')

[giorgiatosoni]

Still an issue also for me. Any news?

[jasonleongbio]

Trying out the tutorials these days and it seems this issue still persists.

---

Here is what I got from running the tutorial pbmc3k.ipynb:
Before writing the AnnData object to a .h5ad file (after the PCA step; before computing the neighborhood graph)

• Inside adata.uns:

OverloadedDict, wrapping:
	OrderedDict([('log1p', {'base': None}), ('hvg', {'flavor': 'seurat'}), ('pca', {'params': {'zero_center': True, 'use_highly_variable': True}, 'variance': array([ (not showing the numbers for simplicity here) ],
      dtype=float32), 'variance_ratio': array([ (not showing the numbers for simplicity here) ],
      dtype=float32)})])
With overloaded keys:
	['neighbors'].

---

After loading the matrix from the .h5ad file:

• Inside adata.uns, the log1p key became an empty dictionary:

OverloadedDict, wrapping:
	{'hvg': {'flavor': 'seurat'}, 'log1p': {}, 'pca': {'params': {'use_highly_variable': True, 'zero_center': True}, 'variance': array([ (not showing the numbers for simplicity here) ],
      dtype=float32), 'variance_ratio': array([ (not showing the numbers for simplicity here) ],
      dtype=float32)}}
With overloaded keys:
	['neighbors'].

[m21camby]

Although adata.uns['log1p']["base"] = None seems work for tl.rank_genes_groups the results is weird in my analysis. When I check, logfoldchange, values didn't make any sense. Some of them are almost near 100. Is there any case also or maybe I'm wrong.

[lubianat]

Just to let you know that the same issue happened here when running the tutorial with my data.

[KoichiHashikawa]

Same here. adata.uns['log1p']["base"] = None eliminated the error, but the FC seems weird.
I compared the FC results with Seurat FindMarker results, which used the same FC calcualtion. For most genes, Scanpy resulted in much higher FC (some gets 30 or more), which I have never seen.

[KoichiHashikawa]

@LuckyMD requires attentions to several of the threads above from Scanpy team.
Thanks!

[zhenxingjian]

Same error here.

[flying-sheep]

Duplicate of scverse/anndata#673

I have a fix waiting in scverse/anndata#999