How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

[vagabond12]

the deg gene list from seurat

gene list input to clusterProfiler compareCluster

Thank you

[Pancreas-Pratik]

Hey @vagabond12,

I think you may have posted this on Biostars as well.

Here is a way to do it for your reference: https://www.biostars.org/p/438566/#493549

[apal6]

Hi,

I used your script to perform enrichment but it is not able to map, here is the code and error:

dfsample$0 = bitr(dfsample$0, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db")

'select()' returned 1:1 mapping between keys and columns Error in bitr(dfsample$0, fromType = "SYMBOL", toType = "ENTREZID", : (converted from warning) 2% of input gene IDs are fail to map...

I appreciate your help.

Thanks, Aastha

[huerqiang]

@apal6 Setting Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true").