How to deal with the duplicated samples in TARGET-AML?

[xiaolan552]

Hi @tiagochst when I use the TCGAbiolinks to download the TARGET-AML project，I found some samples duplicated，such as: `		cases	experimental_strategy	analysis_workflow_type
101	TARGET-20-PADYIR-09A-01R	RNA-Seq	STAR - Counts
377	TARGET-20-PADYIR-09A-01R	RNA-Seq	STAR - Counts
988	TARGET-20-PAECCE-09A-01R	RNA-Seq	STAR - Counts
1012	TARGET-20-PAECCE-09A-01R	RNA-Seq	STAR - Counts
1105	TARGET-20-PAEERJ-09A-01R	RNA-Seq	STAR - Counts
1107	TARGET-20-PAEERJ-09A-01R	RNA-Seq	STAR - Counts
19	TARGET-20-PAKIWK-09A-01R	RNA-Seq	STAR - Counts
909	TARGET-20-PAKIWK-09A-01R	RNA-Seq	STAR - Counts
323	TARGET-20-PAKVGI-09A-01R	RNA-Seq	STAR - Counts
951	TARGET-20-PAKVGI-09A-01R	RNA-Seq	STAR - Counts	`

I tried to remove the duplicate sample, but when I was about to merge the data，there hava a new error Error in.rowNamesDF<-(x, value = value) : invalid 'row.names' length

This is my code： query.exp <- GDCquery( project = “TARGET-AML”, data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts", ) query.exp$results[[1]] <- query.exp$results[[1]][!duplicated(query.exp$results[[1]]$sample.submitter_id),] GDCdownload(query.exp) gene.data <- GDCprepare(query = query.exp)

The TCGAbiolinks package version is 2.25.3，R version is 4.2.0.

Any help would be appreciated ! thank you !