Gene Enrichment (GO) and KEGG analysis problems

Question

[ymervenuryavuz]

Hello, I am trying to enrich some sets of genes that was given in a form .txt without their gene IDs. I uploaded the list to RStudio, I installed Bioconducter and clusterProfiler for gene enrichment (GO) and KEGG analysis. But, I couldn't write commands with enrichGO function. Either my arguments was wrong or the list I uploaded was missing something. I don't know the problem and how to fix the problem. Could anybody please help me? Mervenur

[Fabio Marroni]

Which organism?

some sets of genes that was given in a form .txt without their gene IDs

I hope they gave you some sort of gene names. Try to search for the gene names that are in your txt file in RefSeq and ncbi and see if you are able to convert them to the convention required by clusterProfiler. you may also want to play with biomaRt a bit, it really helped me in gene names conversions a few years ago.

[ymervenuryavuz]

Hi Fabio, Thank you for your reply. The list they gave me only contains miRNA target gene names. I will try to do what you suggested. The targeted genes is for the organism called Ambystoma maxicanum.