What kind of expression values as input?

cansysbio / ConsensusTME

ConsensusTME Gene Sets and R Script

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What kind of expression values as input? #2

Closed komalsrathi closed 4 years ago

komalsrathi commented 4 years ago

Hi!

I am going to try ConsensusTME. I might have missed it in the README/publication but cannot find as to what kind of expression values are allowed as input: FPKM/log2 counts/raw counts/TPM?

Please let me know.

Thanks!

olliecast commented 4 years ago

Hi Komal,

We currently consider TPM to be the best input for the ssGSEA framework since it best captures the relative abundance of different gene expression.

We haven't however benchmarked this (something on my to do list).

Ollie