Question: TCGA PRAD Biochemical Recurrence Data Problem
0
gravatar for Andy Lee
18 months ago by
Andy Lee10
Andy Lee10 wrote:

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
ADD COMMENTlink modified 4 months ago by Yijun Tian20 • written 18 months ago by Andy Lee10

@Andy Lee

Hi Andy,

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

Yijun

ADD REPLYlink written 4 months ago by Yijun Tian20

Are the day values positive or negative?

Here is the official definition of the days_to_first_biochemical_recurrence field: h

ADD REPLYlink written 4 months ago by Kevin Blighe41k
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