TCGA PRAD Biochemical Recurrence Data Problem

Question

[Andy Lee]

I downloaded the TCGA prostate adenocarcinoma clinical data from the following url:

https://xenabrowser.net/datapages/?dataset=TCGA.PRAD.sampleMap/PRAD_clinicalMatrix&host=https://tcga.xenahubs.net

In the clinicalMatrix file, the "biochemical_recurrence" field for the following sample ids are all "NO", presumably indicating that these samples did not have biochemical recurrence. However, their "days_to_first_biochemical_recurrence" are not 0. Could somebody please explain if this is an error? Should I assume that because the "days_to_first_biochemical_recurrence" exists the sample actually had BCR?

• TCGA-EJ-5524-01
• TCGA-G9-6339-01
• TCGA-G9-6498-01
• TCGA-HC-7741-01
• TCGA-HC-7821-01
• TCGA-J4-A67S-01
• TCGA-J4-A6G3-01
• TCGA-J4-AATZ-01
• TCGA-J9-A52B-01
• TCGA-J9-A52E-01
• TCGA-KK-A7AQ-01
• TCGA-KK-A7AU-01
• TCGA-KK-A7AY-01
• TCGA-KK-A7B0-01
• TCGA-KK-A8I4-01
• TCGA-KK-A8I7-01
• TCGA-V1-A8MJ-01
• TCGA-V1-A8MU-01

For other sample ids where the "biochemical_recurrence" is "NO", the "days_to_first_biochemical_recurrence" is absent or NaN.

Also, the following sample ids' "biochemical_recurrence" field is NaN, but the "days_to_first_biochemical_recurrence" is not absent or NaN. What should I do for these samples?

• TCGA-G9-6332-01
• TCGA-HC-7212-01
• TCGA-HC-7232-01
• TCGA-HC-7738-01
• TCGA-M7-A722-01

[Yijun Tian]

@Andy Lee

Hi Andy,

I noticed same problems for the biochemical recurrence data. Do you have a answer now?

Yijun

[Kevin Blighe]

Are the day values positive or negative?

Here is the official definition of the days_to_first_biochemical_recurrence field: