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The dataframe contains duplicate samples #1

@LuigiSantise99

Description

@LuigiSantise99

I encountered a problem when downloading CNV data for LGG. The operation is not completed because there are multiple rows with the same sample (duplicated unique identifiers).
How can I handle the problem to get the same results as yours?

Error on terminal:

|     |cases                                                     |experimental_strategy |analysis_workflow_type |
|:----|:---------------------------------------------------------|:---------------------|:----------------------|
|859  |TCGA-CS-4938-10A-01D-1892-01;TCGA-CS-4938-01B-11D-1892-01 |Genotyping Array      |ASCAT2                 |
|861  |TCGA-CS-4938-10A-01D-1892-01;TCGA-CS-4938-01B-11D-1892-01 |Genotyping Array      |ASCAT3                 |
|498  |TCGA-CS-4941-01A-01D-1466-01;TCGA-CS-4941-10A-01D-1466-01 |Genotyping Array      |ASCAT2                 |
|500  |TCGA-CS-4941-01A-01D-1466-01;TCGA-CS-4941-10A-01D-1466-01 |Genotyping Array      |ASCAT3                 |
[...]
|1559 |TCGA-WY-A85C-10A-01D-A366-01;TCGA-WY-A85C-01A-11D-A36N-01 |Genotyping Array      |ASCAT2                 |
|1561 |TCGA-WY-A85C-10A-01D-A366-01;TCGA-WY-A85C-01A-11D-A36N-01 |Genotyping Array      |ASCAT3                 |
|1345 |TCGA-WY-A85D-01A-11D-A36N-01;TCGA-WY-A85D-10A-01D-A40C-01 |Genotyping Array      |ASCAT2                 |
|1347 |TCGA-WY-A85D-01A-11D-A36N-01;TCGA-WY-A85D-10A-01D-A40C-01 |Genotyping Array      |ASCAT3                 |
|832  |TCGA-WY-A85E-10A-01D-A366-01;TCGA-WY-A85E-01A-11D-A40C-01 |Genotyping Array      |ASCAT3                 |
|1157 |TCGA-WY-A85E-10A-01D-A366-01;TCGA-WY-A85E-01A-11D-A40C-01 |Genotyping Array      |ASCAT2                 |
Error in GDCprepare(query.cnv, save = TRUE, save.filename = paste0("./data/TCGA-",  :
  There are samples duplicated. We will not be able to prepare it
Execution halted

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