单细胞测序数据差异基因KEGG富集分析

单细胞测序数据分析时，差异基因/marker 基因功能GO/KEGG富集分析，执行此代码Rscript $scripts/enrichKEGG_pip.r --gene.list FindMarkers.deg.Enterocyte.AvsB.tsv -o KEGG -n deg.Enterocyte.AvsB --pvalueCutoff 0.05 --ann.db org.Ss.eg.db --organism ssc --idtype SYMBOL报错：nohup: ignoring input

Failed to create bus connection: No such file or directory

please set right --idtype you input to analysis, The example ID types below are supported:

[1] "ACCNUM" "ALIAS" "ENTREZID" "ENZYME" "EVIDENCE"

[6] "EVIDENCEALL" "GENENAME" "GO" "GOALL" "ONTOLOGY"

[11] "ONTOLOGYALL" "PATH" "PMID" "REFSEQ" "SYMBOL"

[16] "UNIGENE" "UNIPROT"

'select()' returned 1:1 mapping between keys and columns

Reading KEGG annotation online:

--> No gene can be mapped....

--> Expected input gene ID:

--> return NULL...

NULL

Error in (function (classes, fdef, mtable) :

unable to find an inherited method for function ‘dotplot’ for signature ‘"NULL"’

Calls: dotplot -> <Anonymous>

Execution halted

想请教下老师问题在哪？应该怎么解决？因为GO分析就正常分析，没有报错，KEGG富集分析却出现问题。麻烦老师解答，谢谢老师。

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2 个回答

omicsgene - 生物信息 2024-06-11 10:17

擅长：重测序,遗传进化,转录组,GWAS

目前只支持人和小鼠，其他物种不支持；

非模式物种KEGG GO富集分析可以看看这个课程：

组学大讲堂发现一节好课

RNAseq有参转录组数据自主分析

点击课程：https://bdtcd.xetslk.com/s/29EigM

 2024-07-03 21:44

老师，我参考了这个课程依然报错，Failed to create bus connection: No such file or directory