Two days_to_last_followups encountered when conducting Survival Analysis with TCGA Clinical Data
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3 months ago
yukinoyou • 0

I was conducting Survival Analysis to TCGA-LIHC project, and when I look through the clinical data I found that there are two days_to_last_followups tags. One of it belongs clin_shared:race_list,and the other lihc:follow_ups

one that belongs to clin_shared:race_list

<clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="999" cde_ver="1.000">438</clin_shared:days_to_last_followup>

one that belongs to lihc:follow_ups

<clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="999" cde_ver="1.000">500</clin_shared:days_to_last_followup>

they have different values, and I wonder which one should I take?

thanks so much

TCGA Clinical • 487 views
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Looks like you are checking the clinical XML files. Could you point to the exact file(s) that have the issue?

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Sorry for my untimely reply, the file that have the issue is

807f276b-509b-4d4f-80ab-f7189c9f98a4/nationwidechildrens.org_clinical.TCGA-CC-A123.xml

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Got an answer from an expert

  • One of the days_to_last_followup has a precision of month and a value of -8 . This also seems to be under some subheader called “additional_studies” which I’m not too familiar with.
  • The other has a precision of day and a value of 219
  • GDC seems to have imported 219. That would be my recommendation too.
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