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



attachments-2020-02-XzBURxRk5e3e82d667701.png
帮助!谢谢

问题补充:

attachments-2020-02-TcrV8gnJ5e40e5a483d9d.pngattachments-2020-02-usTAS8Jp5e40e5b1321c7.png--------------------------------------------------------

按照前辈 给的代码删除数据重新跑了一遍,结果:

attachments-2020-02-gkVjttFP5e4144a58559f.png

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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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  • 带带大学习 提出于 2020-02-08 17:44