Please make sure these conditions are met
What happened?
When I used sc.pp.scale(adata_filtered, max_value=10, layer='log1p_norm')to specify scaling the 'log1p_norm layer', I found that the function output was not stored by default in .X, but instead overwrote the 'log1p_norm' layer. When I did not specify a layer and used the default adata_filtered.X with sc.pp.scale(adata_filtered, max_value=10, layer=None), the output correctly updated adata_filtered.X
Minimal code sample
#The following code will reproduce the described issue
sc.pp.normalize_total(adata_filtered,target_sum=1e4,layer=None)
sc.pp.log1p(adata_filtered,base=None,layer=None)
adata_filtered.layers['log1p_norm']=adata_filtered.X.copy()
sc.pp.highly_variable_genes(adata_filtered,n_top_genes=2000,batch_key='Sample',layer='log1p_norm')
sc.pp.scale(adata_filtered,max_value=10,layer='log1p_norm')
#The issue will not occur after modifying the layer parameter of sc.pp.scale layer=None instead of layer='log1p_norm'
sc.pp.normalize_total(adata_filtered,target_sum=1e4,layer=None)
sc.pp.log1p(adata_filtered,base=None,layer=None)
adata_filtered.layers['log1p_norm']=adata_filtered.X.copy()
sc.pp.highly_variable_genes(adata_filtered,n_top_genes=2000,batch_key='Sample',layer='log1p_norm')
sc.pp.scale(adata_filtered,max_value=10,layer=None)
Error output
Versions
| Dependency |
Version |
| lazy_loader |
0.4 |
| psutil |
7.2.1 |
| asttokens |
3.0.1 |
| pytz |
2025.2 |
| llvmlite |
0.46.0 |
| numba |
0.63.1 |
| prompt_toolkit |
3.0.52 |
| stack-data |
0.6.3 |
| debugpy |
1.8.19 |
| tornado |
6.5.4 |
| PyYAML |
6.0.3 |
| decorator |
5.2.1 |
| patsy |
1.0.2 |
| natsort |
8.4.0 |
| executing |
2.2.1 |
| parso |
0.8.5 |
| pyarrow |
22.0.0 |
| six |
1.17.0 |
| charset-normalizer |
3.4.4 |
| setuptools |
80.9.0 |
| cycler |
0.12.1 |
| joblib |
1.5.3 |
| python-dateutil |
2.9.0.post0 |
| ipython |
8.37.0 |
| statsmodels |
0.14.6 |
| kiwisolver |
1.4.9 |
| wcwidth |
0.2.14 |
| leidenalg |
0.11.0 |
| pillow |
12.1.0 |
| pure_eval |
0.2.3 |
| igraph |
1.0.0 |
| h5py |
3.15.1 |
| texttable |
1.7.0 |
| pynndescent |
0.5.13 |
| jedi |
0.19.2 |
| Component |
Info |
| Python |
3.10.19 |
| OS |
Linux-5.15.0-86-generic-x86_64-with-glibc2.35 |
| CPU |
96 logical CPU cores, x86_64 |
| GPU |
No GPU found |
| Updated |
2026-01-07 17:20 |
