Question: question about survival analysis
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gravatar for tujuchuanli
6 months ago by
tujuchuanli40
tujuchuanli40 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 6 months ago • written 6 months ago by tujuchuanli40

Thanks, Kevin. I will check it now~~

ADD REPLYlink written 6 months ago by tujuchuanli40
0
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe42k
Republic of Ireland
Kevin Blighe42k 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 counts, which are produced from the normalised counts in DESeq2: Extracting transformed values

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe42k
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