Question: survival analysis of TCGA data
gravatar for monukmr98
5.3 years ago by
United States
monukmr9860 wrote:

hi there

I am doing some survival analysis on TCGA patients of my interest. I have to draw Kaplan-meier curve, which I am able to do with "survival" package in R using their default "aml" data. Same format I applied on my samples' data and got some curve. But, I have doubt whether I am doing it right way or not. 

eg. survival package has default data format as follows

> aml
   time   status          x
1     9      1    Maintained
2    13      1    Maintained
3    13      0    Maintained


and my prepared data format for GBM tissue samples is as follows

     time         status      x
1    11.9333      1    class1
2    4.8000      1    class2
3    18.6000      1    class1


I have doubt regarding status tag (middle column i.e. all are 1 ) in my data; as my data does not contain information of censored subjects. I have taken all dead patients and time is reported in months for corresponding dead patients (days_to_death column). All this data has been taken from *clinical_patient_gbm.txt file. So my question is "Am I MISSING SOMETHING" ? like "Censored data". If yes, then how to obtain censored data from TCGA and from which file (followup file)?



ADD COMMENTlink written 5.3 years ago by monukmr9860

why have you biased the dataset to the dead individuals only? Have a look for days_to_last_follow_up or similar to complement your current dataset

ADD REPLYlink written 5.3 years ago by russhh5.2k

you mean he should add the 'days_to_last_follow_up' to the current dataset as censored data(status is '0')?

ADD REPLYlink written 5.2 years ago by Miao Yu80
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