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
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: