Hello everyone.
I'm writing to ask a question about the calculation of the gene signature score.
Specifically, I want to classify TCGA samples by using an “effector CD8+ T cell signature score” as an index. (I'm planning to use already-established gene lists.)
I searched the literature that describes how to calculate the score and came up with the following:
Integrative clinical genomics of metastatic cancer. Robinson et al. Nature 2017.
https://www.nature.com/articles/nature23306
According to this paper, calculation method is explained as follows;
The expression of each gene in the pathway was transformed into percentiles and the activity of each pathway was calculated as the average percentile score of all genes in a pathway minus 50 (that is, the expected median activity of a pathway).
Is this calculation method widely applicable?
I am a beginner in the field of informatics, so I would appreciate it if you could point out any misunderstandings.
Sincerely,
