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YuLab-SMU / ReactomePA

Reactome Pathway Analysis
https://yulab-smu.top/biomedical-knowledge-mining-book/
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No gene can be mapped, return NULL #17

Closed ulapei closed 6 years ago

ulapei commented 6 years ago

Hi!

I am very new to Reactome and Pathway Analysis. I have a .csv file that contains only gene IDs in the Entrez form. I.e. "23956”, “56277”, “12268”, “20259”, “16157”, “11815". However, whenever I try to run the enrichPathway function, I get the error: --> No gene can be mapped.... --> Expected input gene ID: 12491,74030,100502803,27801,12727,208092 --> return NULL...

The organism that I'm working with is mouse and the function I am using is: x <- enrichPathway(gene=mydata,organism = "mouse", readable=T)

I have checked the IDs in KEGG and it does recognize the genes and the data associated with it. I'm really struggling to understand what could be causing the issue. Thanks!

I have also tried it with data that includes the logFC and p values, but get the same error.

ulapei commented 6 years ago

Solved it by converting the data into values. Thanks, it works now.

Dmy1999 commented 2 years ago

could you plz be more specific on how to resolve this problem, cause l'm also puzzled here.