if living, the time-to-death usually refers to last follow-up time. it's
just censored in cox model.
However, the first patient example indeed looks suspicious to me:
days_to_death vital_status
days_to_tumor_recurrence
TCGA.20.0990 789 living 870
if this patient has been followed up in the 870-th day, determining
recurrence yes/no, then the last follow-up date should be at least 870; in
another word, I always expect time-to-death or last follow-up larger or
equal to time-to-recurrence.
it'll be more informative to print out recurrence_status as well.
Chen
On Tue, May 20, 2014 at 4:00 AM, Dario Strbenac
<dstr7...@uni.sydney.edu.au>wrote:
> library("curatedOvarianData")
> data(TCGA_eset)
> clinical <- pData(TCGA_eset)[, 1:20]
> alive <- clinical[clinical[, "vital_status"] == "living", ]
> head(alive[, c("days_to_death", "vital_status",
> "days_to_tumor_recurrence")])
>
> days_to_death vital_status days_to_tumor_recurrence
> TCGA.20.0990 789 living 870
> TCGA.23.1118 2616 living 2616
> TCGA.23.1026 816 living 797
> TCGA.20.0991 797 living 797
> TCGA.23.1119 3953 living 3378
> TCGA.23.1028 1503 living 133
>
> I thought days_to_death would be NA for living samples. The first sample
> has a recurrence time larger than the days to death. I realise that
> days_to_death can also contain time to last follow-up, but then why isn't
> it the same as days_to_tumor_recurrence, for the first sample ?
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
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> Bioc-devel@r-project.org mailing list
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