'Warning message' Error in DESeq2 with Samples Already Analysed Before


I am relatively new to bioinformatics and I am currently running some featureCounts count tables through DESeq2 for DGE analysis. I have 4 groups (WT baseline, WT 1h, Mutant baseline, Mutant 1h), containing 4 samples each (2 males & 2 females).

I previously ran WT baseline vs WT 1h, Mutant baseline vs Mutant 1h, and WT baseline vs Mutant baseline, specifying Factor 1 as these comparisons with their respective levels, and Factor 2 as ‘Sex’ (with Males vs Females as factor levels) to control for differences in sex. This means all my samples went through at least 1 round of analysis already with no problems whatsoever. However, when I tried my last comparison, WT 1h vs Mutant 1h, controlling the same way for sex, and using all of the same settings and parameters, I received the following error message and the job was not executed:

An error occurred with this dataset:
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 str2lang(x) : :1:10: unexpected symbol
1: ~ Sex + 1h
Calls: as.formula → formula → for

I can’t really decipher what this message means, and I am quite baffled since I already ran analyses on these groups with the same parameters and no problems arose. This excludes problems with my featureCounts count table and its formatting. It must be something else, so I would really appreciate any help.


I think it happens because you have the value “~ Sex + 1h” somewhere in your input file. Did you had this also in your other files?

Would it be possible for you to change “~ Sex + 1h” to “Sex1h” and check if the error comes up again? There are tools in galaxy that can replace text, you can search for “replace” in the tool menu.