Clusterprofiler - best practise for missing ids
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paun_bio • 0
@723ff6f8
Last seen 10 months ago

Hi,

i have prepared a list for the use in clusterprofiler as described in the manual. Sorted by FC and converted from Ensembl Gene ID to NCBI gene ID. Some ENSEMB Gene IDs do not have a mapping NCBI id and are left with an NA.

gene IDs: 27253 NA NA 10529 5737 3306

FC: 3.38448326 2.77771269 2.70673338 2.31221944 2.22218971 2.04982881

I'm wondering what is the best practices here regarding filtering of those genes.

  1. Remove genes prior to enrichment.
  2. Keep genes for enrichment.

Thanks for any help!

ReactomePA clusterProfiler GeneSetEnrichment • 167 views
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