Open loganylchen opened 1 year ago
Hi Logan,
Thanks for your commit, but I am considering removing these function, calculating the TPM or FPKM seems useless?
Yanshuo
Hi Yanshuo,
I don't have any solid evidence for the necessity of converting counts to TPM or FPKM. But I saw many other deconvolution tools accept raw counts as their first priority input format.
Considering the pseudo-bulk differential expressed gene identification in general single-cell analysis, I think it should be OK, or reasonable to treat the count matrix from both single-cell and bulk RNA-seq following the same distribution. Maybe we could have some tests if the predictions perform better with/without transforming.
Logan
No need to calculate the gene len if the file already provided.