Here, I want to analyze the differential expressed genes (DEGs) in TCGA dataset. I use edgeR to identify DEGs and use the TMM normalization method.
Next, I want to perform survival analysis using DEGs. The equation for the model is “coxph(Surv(time,censor) ~ exprs)”, where time is survival time (for dead patients) or last follow up time (for alive patients), censor is dead or alive (alive=0 and dead=1) for each cancer sample, and exprs is the gene expression value measured by TMM normalization.
I searched the literature and found that no paper used expression value by TMM normalization in survival model. However I wanted to use a consistent measurement of gene expression from identification of DEGs to survival analysis. Is it proper to use expression value by TMM normalization in survival analysis?