使用"TCGAbiolinks"下载时遇到报错如下

Question

library("TCGAbiolinks")
library("dplyr")
library("DT")
library("SummarizedExperiment")

cancer_type <- "TCGA-LUAD"
data_type <- "Gene Expression Quantification"
data_category <- "Transcriptome Profiling"
workflow_type <- "HTSeq - FPKM"

Expr_df <- GDCquery(project = cancer_type,
                    data.category = data_category,
                    data.type = data_type,
                    workflow.type = workflow_type)

GDCdownload(Expr_df,method = "api",files.per.chunk = 6)

expdat<- GDCprepare(query = Expr_df) 

报错如下

> expdat<- GDCprepare(query = Expr_df) 
|================================================================================|100%                      Completed after 57 s 
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
luad subtype information from:doi:10.1038/nature13385
From the 60483 genes we couldn't map 3881
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : 
  Failed to find a rowRanges() method for RangedSummarizedExperiment objects.

请问该如何解决？

Answer 1

检查是不是TCGAbiolinks版本问题，卸载后通过BiocManager安装一下试试。
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("TCGAbiolinks")