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Dear all,
First of all thank you for writing and maintaining such a useful resource!
In this issue MAST developers are suggesting using log2(counts +1) as input. In book however, data were normalised (sc.pp.normalize_total(adata, target_sum=1e6)). Does that violate the MAST assumption as mentioned here:
First make sure you have the latest MAST version from GitHub.
MAST does normalization through the cngeneson model component. It's not clear to me that feeding it prenormalized log2 expression will still allow the model to behave as expected.
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Dear all,
First of all thank you for writing and maintaining such a useful resource!
In this issue MAST developers are suggesting using log2(counts +1) as input. In book however, data were normalised (
sc.pp.normalize_total(adata, target_sum=1e6)
). Does that violate the MAST assumption as mentioned here:Thank you and kind regards
Amel Zulji
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