Normalization of the matrix

[michela12345]

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]

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.