Can I use TCGA's TPM data format for bulk RNA as input to bisque?

cozygene / bisque

An R toolkit for estimation of cell composition from bulk expression data

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Can I use TCGA's TPM data format for bulk RNA as input to bisque? #40

Closed suhuanhou closed 9 months ago

suhuanhou commented 10 months ago

Looking forward to the author's answer, thanks!

brandonjew commented 9 months ago

Hi @suhuanhou,

Thank you for your interest in our method! Bisque expects a counts matrix and internally performs CPM normalization. While applying CPM normalization on top of TPM normalization gives you the same TPM values, the results in the manuscript are based off of CPM normalization alone. Bisque's behavior with TPM values has not been tested and we suggest adhering to the raw counts input.

Best, Brandon