How to change from gene_id to GeneID/EntrezID using R

Question

[Nicolas]

Hello im currently doing a differential expression analysis and the identifiers im using are gene_id's, but to do the GO enrichment analysis and the domain anotation i need to have them in GeneID which according to what I have investigated is the same EntrezID. I already looked for online tutorials but all of them are oriented to change between ENSMBL_ID's and EntrezID so i dont know how to exactly change my identifiers using R

[Shred]

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[Nicolas]

The thing is that every tutorial i've seen here is about using biomrt but as i said my data are not related to ENSMBL and i dont have the capacity toi re run the program i used to get the counts, also im not working with any model organism

Answer 1

[Kevin Blighe]

Hello,

A solution that may help: Translating gene names to entrez id's

By the way, if you are using topGO for the enrichment, then it accepts all of these identifiers: "entrez", "genbank", "alias", "ensembl", "symbol", "genename", and "unigene". I have posted soem convenient code for enrichment again GO BP, here: GO analysis using topGO

Kevin

[Nicolas]

Thank you for your help but my data are not related to ENSMBL and im not working with any model organism that allow me to use the org packages, Maybe you know another way to do that?

[Kevin Blighe]

It would have been good if you had mentioned the species in your opening question.