Hi everybody! I am trying to do survival analysis with TCGA-PRAD data. I learned how to do overall survival, KM plots and cox regression following this tutorial: https://bioconnector.github.io/workshops/r-survival.html , in which you learn how to use R packages "survival", "survminer" and TCGA data using the package "RTCGA".
My aim now is to do disease-free survival, but looking at the clinical data that i can download with RTCGA, I can't understand which columns I have to use, I can't see a clear indication of dfs. Also, checking here on biostars it seems that there are no other questions related specifically to it.
Can someone please help me to find a way to do this? Some example code will be really appreciated! Thank you a lot!!
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mario.red8976
Hello, I don't know RTCGA.
The events of DFS is progress/recurrent so you need to find which column contains this information. I personally suggest you download clinical data from cBioportal, and you will get 2 columns Disease Free (Months) and Disease Free Status.
BTY, I did DFS for TCGA-PRAD before and it seems too little event cases. You can try.
Hi, thank you for your answer! The problem is that in PRAD, there are very few death events (like 10 in 500 cases) so I don't think that doing overall survival will give good results with this dataset, so I thought that DFS might be better.
Ok, I'll try pfs, thank you!
why the DFS is different in TCGA and cbioportal?
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Hi @miky.zo ! Have you solved your problem?I now met the same question with you.I downloaded BLCA clinical data via TCGA-Assembler but I don't know how to get DFS(disease-free survival). I only know the OS(overall survival) is merge days_to_last_followup and days_to_death but have no idea about anything like progress/recurrent. Besides, after I read @MatthewP 's reply I am confused why the DFS in TCGA and cbioportor are different?
Why did you delete this and other posts of yours, mario.red8976 ?