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counts_per_cell has no effect on pp.normalize_per_cell(adata)

See original GitHub issue

counts_per_cell has no effect on pp.normalize_per_cell(adata) as it is overwritten here:

https://github.com/theislab/scanpy/blob/e0d2ea60fa2394f1158618bc69dff4fc639b51c4/scanpy/preprocessing/_simple.py#L599

Would be great if one could use, e.g. the initial cell size (from before filtering). Note, that this issue only holds when passing AnnData. With AnnData.X it works fine.

Issue Analytics

State:
Created 5 years ago
Comments:23 (21 by maintainers)

Top GitHub Comments

1reaction

LuckyMDcommented, Jul 15, 2020

Indeed, scran often works better than CPM normalization. I would recommend to use it via anndata2ri or rpy2 as I demonstrate in the case study with the paper. You can find that [here] (https://github.com/theislab/single-cell-tutorial/blob/master/latest_notebook/Case-study_Mouse-intestinal-epithelium_1906.ipynb)

1reaction

LuckyMDcommented, Mar 5, 2019

I will put it on my long list of potential HiWi topics…

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