Question: question about survival analysis
0
gravatar for tujuchuanli
18 months ago by
tujuchuanli60
tujuchuanli60 wrote:

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

ADD COMMENTlink modified 18 months ago • written 18 months ago by tujuchuanli60

Thanks, Kevin. I will check it now~~

ADD REPLYlink written 18 months ago by tujuchuanli60
3
gravatar for Kevin Blighe
18 months ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

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

ADD COMMENTlink modified 6 months ago • written 18 months ago by Kevin Blighe60k
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