# Missing gene id labeling in limma

**URL:** <https://help.galaxyproject.org/t/missing-gene-id-labeling-in-limma/14772>\
**Category:** usegalaxy.org.au support\
**Tags:** limma\_voom\
**Created:** [February 18, 2025, 12:57am UTC](https://help.galaxyproject.org/t/missing-gene-id-labeling-in-limma/14772 "2025-02-18T00:57:30Z")\
**Posts on this page:** 1\
**Showing post:** 13

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 24, 2025, 6:29pm UTC](https://help.galaxyproject.org/t/missing-gene-id-labeling-in-limma/14772/13 "2025-02-24T18:29:27Z")

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Hi @Jeff

Ok – I see the problem now.

Some of the Bioconductor tools do not understand the “dot” in identifiers. Sort of a gotcha but that is how the tools work everywhere. In short, R is interpreting the dot when it shouldn’t be. I think you can quote it but I haven’t tested that with every tool in this pipeline.

We have a few topics about it if you are curious. The solution can be to remove the `.N` part of the identifier. This is one example.

- [how to replace these ID with official gene names?](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726)

The FAQ here has a troubleshooting warning but it is easy to miss!

- [FAQ: Extended Help for Differential Expression Analysis Tools](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html)
  - Sometimes these tools do not understand `transcript_id.N` and `gene_id.N` notation (where N is a version number).
  - This notation could be in fasta or tabular inputs.
  - Try [removing `.N` from all inputs](https://training.galaxyproject.org/training-material/search2.html?query=olympics), and check for the accidential creation of new duplicates!

This trips up people using the tools directly, too!

- [https://support.bioconductor.org/post/search/?query=version+numbers+on+identifiers](https://support.bioconductor.org/post/search/?query=version+numbers+on+identifiers)

But I’m glad you were able to get this working! You might be able to get the other annotation sources working too. 🙂

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_[View the full topic](https://help.galaxyproject.org/t/missing-gene-id-labeling-in-limma/14772)._