Normalizing expression values
Entering edit mode
7 weeks ago
mt_pereira • 0

Hello everyone!

I am starting out with scRNA-seq preprocessing and quality control analysis through Scanpy.

I have found a tutorial and 2 of the steps are not completely clear for me and I would like to ask if anyone could help me out.

The first step that I do not get is the conversion of the count matrix into layers.

The second is related to normalization - in two different tutorials I have found two different methods for normalization and I do not know which one is more adequate or if it does not make such a difference. The 2 commands are the following:

sc.pp.normalize_per_cell(adata, counts_per_cell_after=1e4)
sc.pp.normalize_total(adata, target_sum=1e4)

Thank you so much in advance for your help!

normalization Scanpy logCPM scRNA • 166 views

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