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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Per cell normalization #56

Closed JSchapke closed 4 years ago

JSchapke commented 4 years ago

In the normalize_per_cell function, you normalize the matrix by rows and then multiply the results by 1e6. What is the purpose of the multiplication?

lucapinello commented 4 years ago

This is essentially the idea behind the TPM (transcript per millions). It is better to have larger numbers to avoid machine precision errors propagating in downstream analysis.