question about survival analysis

Question

[tujuchuanli]

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?

Thanks

Answer 1

[Kevin Blighe]

You could get ideas from this tutorial: Survival analysis with gene expression

For this, however, I would use the regularised log (rlog) or variance stabilised expression levels, which are produced from the normalised counts in DESeq2: Extracting transformed values

Kevin

[tujuchuanli]

Thanks, Kevin. I will check it now~~