Error in `levels<-`(`*tmp*`, value = as.character(levels)) : factor level [43] is duplicated

[Pravithaks]

What does this error refers to?

GDCdownload(query_samples) rcc = GDCprepare(query_samples) I got this when I ran above command.

please help.

[tiagochst]

Hi, could you send the code for the query argument please?

[Pravithaks]

rcc analysis

library("TCGAbiolinks") library("SummarizedExperiment") library("DESeq2") library(tidyverse)

Genome of reference: hg38

collect all barcodes in the 2 projects

query_all = GDCquery(project = c("TCGA-KIRC","CPTAC-3"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts")

barcodes_all = getResults(query_all, cols=c("cases"))

query_normal = GDCquery(project = c("TCGA-KIRC","CPTAC-3"), data.category = "Transcriptome Profiling", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type=c("Solid Tissue Normal"))

barcodes_normal = getResults(query_normal, cols=c("cases"))

barcodes_samples = barcodes_normal

query_samples <- GDCquery( project = c("TCGA-KIRC"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts",

access = "open",

sample.type=c("Solid Tissue Normal"))

query <- query_samples GDCdownload(query,files.per.chunk = 100) rcc1 <- GDCprepare(query)

query_samples <- GDCquery( project = c("CPTAC-3"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts",

access = "open",

sample.type=c("Solid Tissue Normal"))