Comments (2)
ay-lab
commented on June 3, 2024
This is really a good question. We did an internal comparison (not published) between normalized and raw count compartments. We found that raw count reserves the biological features like laminB1 signal the most. So, we decided to go ahead with raw count compartment analysis. In our dcHiC Nat comm paper https://www.nature.com/articles/s41467-022-34626-6 we captured all the relevant biological features using raw counts. It should also be noted that while doing compartment calling we perform a distance normalization followed by correlation calculation on the raw counts and that probably takes out most of the biases from the data.
Quantile normalization is only to make sure there are no between-sample biases.
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Nico-FR
commented on June 3, 2024
Thank you for the clear answer.
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