Issues in Gene Set Enrichment Analysis using TCGAbiolinks

Question

[ammarsabir15]

I want to perform Gene Set Enrichment Analysis on Glioblastoma Multiforme dataset in TCGA using GO or KEGG pathway. For this purpose I downloaded data from TCGA using this code. `

library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-GBM",
                   data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification")

GDCdownload(query)

This downloaded the data according to the given parameters but when I tried to prepare this query using the command given below :`

 data <- GDCprepare(query)

Then following error came Unable to prepare query there are duplicates in the data. I tried to remove duplicates using fdupes but the software found no duplicate files in the data sets.

So regarding this I have following questions,

• How this error can be removed.?

• For doing enrichment analysis do I need datasets from all workflows i.e HTseq_counts, HTseq_FPKM and HTseq_FPKM_UQ or any one or two from these can suffice?

• Getting the data what are the next steps to perform the enrichment analysis using GO or KEGG pathway ?