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jianhuupenn / TESLA

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
MIT License
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Expression unit of TESLA output #12

Closed nrosewick closed 7 months ago

nrosewick commented 7 months ago

Hello,

I'm wondering what are the unit of the output of TESLA (i.e. enhanced_exp_adata data object) . Is there a way to get (pseudo-)raw counts from it ?

Thank you

jianhuupenn commented 7 months ago

Thanks for your interest in our method. The imputation was conducted at the logged level to better preserve the spatial pattern than UMI count level. You can use the exp function and round function to transform the value back to UMI, but it is not recommended, because there are no constraints on the total UMI count in a sample.