Question: TCGA survival data classification
0
gravatar for archie
15 months ago by
archie100
India
archie100 wrote:

Hello everyone,

I am working on one of the Ovarian cancer TCGA clinical data . I would like to classify patients into two classes based on the survival. I took the column days to death (short : less than three years survival (3653) and long : > 3653 : greater than three year survival and classified the data.

It is also mentioned to use of days to death or days to last follow up for survival analysis (http://www.omnesres.com/tools/tcga/.

I am following one the publication where number of short and long survival are different from my observed count. https://academic.oup.com/jamia/article/22/1/109/832766.

Other study : (147 ST /193 LT )

In my case I have : ( ST 178/166 LT)

In my case, I just took column days to death and classified data into two classes. There are other columns are available such as "yearstobirth" "vitalstatus" "daystodeath" "daystolastfollowup"

I will appreciate all suggestions in case, if my approach need to be adapted.

Thanks

survival tcga • 532 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe67k • written 15 months ago by archie100
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Firstly, I would not worry too much about your patient numbers not matching. The TCGA data is constantly evolving and you will spend days or weeks trying to trace back the discrepancies. Just take the data that you currently have but date-stamp it and provide clear details as to how you obtained it.

With regard to overall survival, you can calculate it as date from pathologic diagnosis to date of death or last follow-up. So:

OS <- as.integer(
  ifelse( is.na(clindata$days_to_death),
    clindata$days_to_last_followup,
    clindata$days_to_death))

For PFS, take a look at the columns:

  • days_to_new_tumor_event_after_initial_treatment
  • days_to_additional_surgery_metastatic_procedure

Kevin

ADD COMMENTlink modified 15 months ago • written 15 months ago by Kevin Blighe67k
1

Thanks alot Kevin. It helped alot.

ADD REPLYlink written 14 months ago by archie100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1981 users visited in the last hour