enrichKEGG "No gene can be mapped"

YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

https://yulab-smu.top/biomedical-knowledge-mining-book/

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enrichKEGG "No gene can be mapped" #689

Open dengzf2021 opened 2 months ago

dengzf2021 commented 2 months ago

R 4.3.3版本，clusterProfiler4.6.0版本，运行以下代码时报错 kegg <- enrichKEGG(gene = id_list$ENTREZID,

organism ='hsa',keyType = "kegg",
pAdjustMethod = "BH",pvalueCutoff = 1,qvalueCutoff = 1,
minGSSize = 10,maxGSSize = 500,use_internal_data = F) --> No gene can be mapped.... --> Expected input gene ID: --> return NULL...

尝试更新clusterProfiler包，提示：载入了名字空间'GOSemSim' 2.24.0，但需要的是>= 2.27.2

于是，安装最新的GOSemSim，又提示：错误: 'namespace:yulab.utils'没有出口'ls2df'这个对象停止执行 ERROR: lazy loading failed for package 'GOSemSim'

请问接下来该怎么处理呢？

dengzf2021 commented 2 months ago

通过更新yulab.utils包解决了安装GOSemSim的问题，但仍然no gene can be mapped

guidohooiveld commented 2 months ago

The first thing you should do is update your Bioconductor packages!

Based on the versions of R and clusterProfiler you mention, it seems you are using the latest version of R, which you installed over your previous version of R, but doing so doesn't update your packages! In other words, your installation of clusterProfiler (and other packages) is outdated.

So type: BiocManager::valid(), and check the output.

Also, next time, please post in English!.