3 TCGAbiolinks使用求助 Downloading genome information (try:0) Using: Human genes (GRCh38.p13) Error: $ operator is invalid for atomic vectors
各位前辈老师们大家好！我在使用TCGAbiolinks包的GDCprepare函数的时候，出现报错，请各位给予分析或者
Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
Downloading genome information (try:0) Using: Human genes (GRCh38.p13)
Error: $ operator is invalid for atomic vectors
Execution halted
帮助！谢谢
问题补充：
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按照前辈 给的代码删除数据重新跑了一遍，结果：
最佳答案 2020-02-17 17:19
刚刚测试了一下，当TCGAbiolinks 为2.10.5版本的时候会报错这样的错误，应该是个bug。建议重新安装TCGAbiolinks 更新到最新版本可以解决以上问题，并且R的版本也更新到最新。
建议把下载的数据全部删除，重新下载数据后再整理，试一下。
query <- GDCquery(project = "TCGA-OV", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", #不同数据解释：https://www.omicsclass.com/article/1059 legacy = FALSE) # 下载数据, 数据比较大，耐心等待 GDCdownload(query = query,directory = "TCGA-OV",files.per.chunk=10, method='api')
gene.data <- GDCprepare(query = query,
save = TRUE,
directory = "TCGA-OV",
save.filename = "TCGA-OV_gene_expression_Counts.rda")
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