Question: Disease Free Survival_ TCGA
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gravatar for mjdm
3 months ago by
mjdm0
mjdm0 wrote:

Hi everybody, I'm trying to study the disease-free survival of PRAD samples from TCGA. I obtained all clinic data but since almost all samples on the 500 available ones are "alive" I thought it was better to focus on disease-free survival more than on Overall Survival. Now I'm stuck since I cannot understand how to handle data to perform this analysis. Suggestion?

Thanks

survival tcga • 148 views
ADD COMMENTlink written 3 months ago by mjdm0

Hi!

Now I'm stuck since I cannot understand how to handle data to perform this analysis. Suggestion?

I am just wondering why you started the analysis if you have no training in this area...? - your supervisor asked you? What data have you already obtained (paste examples)?

ADD REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe61k

Actually yes, my supervisor asked me. I have all the clinic data from TCGA (PRAD) for each sample, so: days to birth, days to death (if available) and their vital status (alive, dead). In theory, the disease-free survival is indicated as a percentage of survival/time. But I would like to know if there are some parameters to take account.

ADD REPLYlink written 3 months ago by mjdm0

You should aim, therefore, to conduct a Cox proportional hazards survival analysis. There are a few different R packages for this, including survminer and survival. There are many examples online. You can adjust for covariates when implementing these models. I am sure that your supervisor can advise on covariates for which to adjust. It's not quite for us to determine this, as we don't know what are the ultimate hypotheses of your work, other than you simply being interested in survival analysis.

ADD REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe61k
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