# rnaseq count files not being recognized by Limma, deseq2, edgeR

**URL:** <https://help.galaxyproject.org/t/rnaseq-count-files-not-being-recognized-by-limma-deseq2-edger/12054>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, transcriptomics\
**Created:** [March 30, 2024, 5:45am UTC](https://help.galaxyproject.org/t/rnaseq-count-files-not-being-recognized-by-limma-deseq2-edger/12054 "2024-03-30T05:45:15Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![squirtle](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/squirtle/32/5371_2.png) [@squirtle](https://help.galaxyproject.org/u/squirtle)\
**Post date:** [March 30, 2024, 5:45am UTC](https://help.galaxyproject.org/t/rnaseq-count-files-not-being-recognized-by-limma-deseq2-edger/12054/1 "2024-03-30T05:45:15Z")

</div>

Hello, I am trying to perform DGE analysis and am able to load my count files as txt or csv. I then change them to tabular file so Limma, dese2, or edgeR can read the datafile.

Warning message:  
In Sys.setlocale(“LC\_MESSAGES”, “en\_US.UTF-8”) :  
OS reports request to set locale to “en\_US.UTF-8” cannot be honored  
Error in eval(ej, envir = levelsenv) : object ‘Control’ not found  
Calls: makeContrasts → eval → eval

- **desc:** Fatal error: Exit code 1 ()
- **error\_level:** 3
- **exit\_code:** 1
- **type:** exit\_code

 ![Screenshot 2024-03-29 at 11.40.25 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/97633fd0c704413340353327786a032769c19a89.png)

txt file first few lines below. Error is the same with or without a column header as above.

 ![Screenshot 2024-03-29 at 11.44.15 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/92dcd6b50fdfac80a99f18053e6f2c426bc0a194.png)

Thank you!

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<div class="post-metadata">

**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:** [April 8, 2024, 9:10pm UTC](https://help.galaxyproject.org/t/rnaseq-count-files-not-being-recognized-by-limma-deseq2-edger/12054/2 "2024-04-08T21:10:08Z")

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> [@squirtle](#):
>
> Error in eval(ej, envir = levelsenv) : object ‘Control’ not found

This means that some data labeled as “Control” was found in one place but not another place.

Guide → [FAQ: Extended Help for Differential Expression Analysis Tools](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html)

If you still need more help, you’ll need to post the full job details from the “i” icon for the error dataset. Details are in the banner at this forum, or see → [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469)