Is CPM matrix acceptable?

dviraran / xCell

Cell types enrichment analysis

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Is CPM matrix acceptable? #59

Open Meijian opened 2 years ago

Meijian commented 2 years ago

For some reason, I only have the CPM matrix as input. Is it reasonable to use CPM as input for xCell? What's the potential problem there?

dviraran commented 2 years ago

No. Needs to be normalized to gene length (TPM, FPKM, etc.).

Meijian commented 2 years ago

Got it, thanks!

Meijian commented 2 years ago

Hi @dviraran, sorry to bother you again, but do you think the output of tximport with "lengthScaledTPM" option would work with xCell. It corrects both gene length and lib size. Or should I calculate TPM by only correcting for gene length? Thanks!