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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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How to deal with batch? #6

Closed millersan closed 3 years ago

millersan commented 3 years ago

Dear authors, Please accept my sincere thanks for providing such a useful tool. Could you tell me how to handle the batch in multiple samples in the cellcall, or I could just use the merged counts in multiple samples? Best, Miller

millersan commented 3 years ago

If I use Seurat, should I use the slot="data" and choose the source = "TPM" or "CPM"?

ShellyCoder commented 3 years ago

Hi millersan,

As far as I know, there are some method, such as Harmony, used to remove batch effect caused by sample source or expriment. But that's not embeded in this R package. You can prepocess the data before input CellCall paclage.

According to Seurat, you can choose source ="CPM" or "TPM". Either is OK.

Hope it may be useful. Shelly.

millersan commented 3 years ago

Dear Shelly, I used source="CPM" and the result is the same as source="TPM". Thank you☺