I have three gene expression signatures and they correspond to three different subtypes. I have a rnaseq data and need to use the three gene signatures to call the three subtypes defined by three gene signatures. What methodologies exist?
Naively i can think of just doing a gsea and based on the score of the gsea, call a sample one subtype and not another. But it's not systematic and can lead to overlaps e.g. for two gene signatures, a single sample can have high score for each if i look at them individually for each sample.
Is there an R code or other knwon methods to handle this situation??