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carmonalab / GeneNMF

Methods to discover gene programs on single-cell data
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normalisation method query #6

Open Shubhra1994 opened 1 month ago

Shubhra1994 commented 1 month ago

Hello, In the html tutorial here the assay used is sct which is sc transformed data.

Is it necessary to use SCT or the lognormalisation pipeline of seurat works well too?

What do you suggest to use?

mass-a commented 4 weeks ago

Hello! we don't have a strong preference/recommendation for the normalization method to apply prior to GeneNMF. The default is "RNA" (standard log-normalization) but also SCT as in the tutorial should work fine. There are several studies comparing normalization methods for scRNA-seq (e.g. https://www.nature.com/articles/s41592-023-01814-1), but I am not aware of any that looks specifically at normalization in the context of NMF. When in doubt, I would go for a simple log-normalization.