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Is CPM matrix acceptable? #59

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Meijian opened this issue Feb 8, 2022 · 3 comments
Open

Is CPM matrix acceptable? #59

Meijian opened this issue Feb 8, 2022 · 3 comments

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@Meijian
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Meijian commented Feb 8, 2022

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
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dviraran commented Feb 8, 2022

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

@Meijian
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Meijian commented Feb 8, 2022

Got it, thanks!

@Meijian
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Meijian commented Feb 11, 2022

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!

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@Meijian @dviraran