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What is wrong with my scripts?

Hi, I have checked with ChatGPT but got no clue. Can anyone help me with this? Thank you very much.

# Prepare the clinical data
> clinical_data <- GDCprepare_clinic(query_clinical, clinical.info = "patient")
  |============                                                            |  17%Error in read_xml.character(xmlfile) : 
  Start tag expected, '<' not found [4]
>
r gdc tcgabiolinks bioconductor
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updated by Ming Tommy Tang Ming Tommy Tang • written by nuorain • nuorain

2 answers

add data.format="bcr xml" in the GDCquery()

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written by Ming Tommy Tang Ming Tommy Tang

Thank you so much. It works now.

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written by nuorain • nuorain

an input file is not a valid XML file.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you for your comments.

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written by nuorain • nuorain

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