What is wrong with my scripts?
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6 weeks ago
nuorain ▴ 30

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 • 426 views
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6 weeks ago
Ming Tommy Tang ★ 4.5k

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

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Thank you so much. It works now.

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1
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6 weeks ago

an input file is not a valid XML file.

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Thank you for your comments.

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