problem in new_tumor_event_after_initial_treatment in XML clinical data

[AlirezaShokrollahi]

Hello When I used TCGAbiolinks for downloading clinical data, I found a problem in XML clinical data. In XML clinical data, There is a column that shows new_tumor_event_after_initial_treatment or new tumor event. For some TCGA projects like TCGA-BRCA, most values in this column are not available or unknown. But in files that we can download from GDC directly, most values in this column are YES or NO. could you help me please and explain what happened. Thank you.

[tiagochst]

Hello,

I need more details to understand the problem. GDC is populated over the XML files.

In XML clinical data, There is a column that shows new_tumor_event_after_initial_treatment or new tumor event.

Which XML file are you looking ? There is a new_tumor_event XML with all the new tumor events information. For TCGA-BRCA there are 91 patients with new_tumor_event: https://rpubs.com/tiagochst/GDC_clinical_indexed_vs_XML

[AlirezaShokrollahi]

Hi I write this code: clinical <- GDCquery(project = "TCGA-BLCA", data.category = "Clinical", file.type = "xml" ) GDCdownload(clinical) clinicalf <- GDCprepare_clinic(clinical, clinical.info = "follow_up")

I look for follow up data in XML files. In follow up data, There is a column that shows new_tumor_event_after_initial_treatment or new tumor event.

I download follow up data from GDC directly and send for you.

you can download follow up data by using TCGAbiolinks and then compare values of that column with follow up data that I sent for you. gdc_download_20200918_165132.755004.tar.gz

[AlirezaShokrollahi]

Thank you I sent more details for you. https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI/issues/58

On Fri, Sep 18, 2020 at 8:44 PM Tiago Chedraoui Silva < notifications@github.com> wrote:

Hello,

I need more details to understand the problem. GDC is populated over the XML files.

In XML clinical data, There is a column that shows new_tumor_event_after_initial_treatment or new tumor event.

Which XML file are you looking ? There is a new_tumor_event XML with all the new tumor events information. For TCGA-BRCA there are 91 patients with new_tumor_event: https://rpubs.com/tiagochst/GDC_clinical_indexed_vs_XML

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[tiagochst]

I need to check better the problem with the XML parsing. But those biotab can be downloaded with TCGAbiolinks with.

query.biotab <- GDCquery(
    project = "TCGA-BRCA", 
    data.category = "Clinical",
    data.type = "Clinical Supplement", 
    data.format = "BCR Biotab")
GDCdownload(query.biotab)
clinical.BCRtab.all <- GDCprepare(query.biotab)

[AlirezaShokrollahi]

Hi Thank you.