Normalization in mean_norm.tsv output

[ajrzepiela]

Dear developers,

What is the meaning of values in mean_norm.tsv file? Values do not sum to 1.0 per cell, when description says that 'file contains the library size-normalized expressions of each cell and gene'. Please explain how I should read the output and if it is possible to transform to smth like TPM.

Thanks,

Andrzej

[gokceneraslan]

mean_norm matrix is library size normalized using normalize_per_cell function from scanpy (https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.normalize_per_cell.html#scanpy.api.pp.normalize_per_cell). I added this to readme file as well.

If you would like to use another normalization method (e.g. TPM), you can use mean.tsv file which is not library size normalized and normalize it manually.