DEseq Error: some values in assay are negative


I am analyzing RNA-seq data and I got stucked in the DEseq because I get the following error:

Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are negative
Calls: get_deseq_dataset … DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet

Does anyone know how to solve it?


Hi Laura,

I got the same error message. Did you sort your issue? could you share any information?


Hi Alessandro,

I forward you the answer of a Galaxy team member:

“I looked at the history and found one minor issue: the option to specify if count files have headers (“Files have header?”) is not set even though they have headers. Whenever there are headers in all counts file, please set this field to “Yes”. Otherwise, just remove the header row in all the counts file and leave this field as “No”.”

So you have to click “Yes” on files have header?when you do the Deseq