For gene set enrichment analysis (GSEA), the software from broad institute does not accept ensemble IDs, I want to do the analysis using entrez ID or hugo ID but about 2000 genes don't have hugo ID or entrez ID.
What should I do?
To lose genes after ID conversion, although annoying, is normal to some extent. But 2000 is a lot. How did you perform the conversion ? What genome is it (species and version) ?
Hi thanks for responding.
It is human all 20000 coding genes. about 2000 is missing after ID conversion. I do the ID conversion using biomart package in R.
I see. A few thoughts:
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