Question: question about survival analysis
0
gravatar for tujuchuanli
2.2 years ago by
tujuchuanli90
tujuchuanli90 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 2.2 years ago • written 2.2 years ago by tujuchuanli90

Thanks, Kevin. I will check it now~~

ADD REPLYlink written 2.2 years ago by tujuchuanli90
3
gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k 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 14 months ago • written 2.2 years ago by Kevin Blighe69k
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