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earmingol / cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
BSD 3-Clause "New" or "Revised" License
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Gene expression normalization #27

Closed joan-yanqiong closed 1 year ago

joan-yanqiong commented 1 year ago

Hi, I want to use the tool with scRNAseq data. Is normalization needed? Or is UMI fine?

earmingol commented 1 year ago

Hi!

It depends on the aggregation method you use for summarizing the expression within a cluster. If you are using an aggregation of the fraction of cells expressing a gene, UMI is fine. However, if you plan to compute the average expression within a cell type, or any other, I recommend using log1p(CPM). The same applies for using distinct communication scores: if you are using continuous ones it's better using log1p(CPM). Also, it is important that your cell type annotation is done after batch-effect correction if you have multiple samples.

I hope this helps!

joan-yanqiong commented 1 year ago

Hi, thank you for the help!