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KChen-lab / METAFlux

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Normalization of the matrix #7

Open michela12345 opened 7 months ago

michela12345 commented 7 months ago

Hey, I have a question: my matrix in the "calculate_reaction_score", considering bulk RNA data, must be normalized? In which way? TMM, TMP,log2? I don't see any directive.

Thank you

LiuCanidk commented 5 months ago

In the original article, the authors used TPM format of NCI-60 cell line and TCGA bulk RNA-seq. So I think it is better to input the TPM value for your expression matrix.