Different clinical results when using GDCprepare_clinic (clinical.info = "patient" vs "follow_up")

[buzhizhang121]

Hollo, When I use GDCprepare_clinic (TCGAbiolinks_2.25.3) to download follow-up data, the results are different. It seems that GDCprepare_clinic(query, clinical.info = "patient") get the earlier version of follow up data.

query <- GDCquery(project = "TCGA-TGCT", data.category = "Clinical", file.type = "xml") GDCdownload(query) ​ cols <- c("bcr_patient_barcode", "vital_status", "days_to_last_followup", "days_to_death") patients <- c("TCGA-2G-AAHL", "TCGA-2G-AAKM") ​

clinical <- GDCprepare_clinic(query, clinical.info = "patient") clinical[clinical$bcr_patient_barcode%in%patients,cols] ​ bcr_patient_barcode vital_status days_to_last_followup days_to_death 56 TCGA-2G-AAHL Alive 1819 NA 64 TCGA-2G-AAKM Alive 2651 NA

clinical2 <- GDCprepare_clinic(query, clinical.info = "follow_up") clinical2[clinical2$bcr_patient_barcode%in%patients,cols] bcr_patient_barcode vital_status days_to_last_followup days_to_death 9 TCGA-2G-AAKM Dead NA 6972 12 TCGA-2G-AAHL Alive 1819 NA 13 TCGA-2G-AAHL Alive 7081 NA

Can you please help to figure out this bug?

Thank you, Yang

[pfren1998]

In the original clinical data from tcga(which is in xml format), there are two records for one patient, it seems that tcga has stored the updated information in the follow_up slot