[Bioc-devel] Contradictory Clinical Data in curatedOvarianData

[Dario Strbenac]

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 ?

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia