Closed millersan closed 2 years ago
If I use Seurat, should I use the slot="data" and choose the source = "TPM" or "CPM"?
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.
Dear Shelly, I used source="CPM" and the result is the same as source="TPM". Thank you☺
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