Should I remove duplicated gene ID before GO enrichment analysis

Question

[hellokwmin]

I am trying to perform GO enrichment analysis.

After DEG analysis, GeneIDs were annotated based on database of Arabidopsis Gene ID (ex: 3435_20010 >>>> ATG3120)

After annotation, I've detected some gene IDs duplicated. Should I remove such duplicated IDs leaving only 1 gene ID before GO analysis?

Answer 1

[Jean-Karim Heriche]

Yes. In general you should remove duplicates because they will affect the outcome. Some tools will either remove duplicates automatically or give an error or warning if they detect duplicates. However there can be situations where one might want to preserve duplicates, typically when the number of occurences of each gene is a meaningful parameter in the experiment.