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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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Normalised data #42

Open Imm123 opened 1 year ago

Imm123 commented 1 year ago

Hi, I would like to ask you about normalisation If I have rawCounts, what do you think it is the best way to do it?

Thanks

ShellyCoder commented 1 year ago

There are two normalization factors, one is the library size of each cell, the other is gene length. Depend on your sequence technology to correct your data. If your data is UMI scRNAseq which is not affected by gene length, you can jues correct library size with CPM.

It's my opinion, wish it provide some help. Best wishes.