DESEQ2 crashing with multiple factors

DESEQ2 ( is running fine while using a single factor. I am running on a local version of Galaxy. However when I run with two factors, DESEQ2 is crashing with error
" ```
Error in row.names<*tmp*, value = value) :
invalid ‘row.names’ length
Calls: rownames<- … rownames<- -> row.names<- -> row.names<

Is there a way to resolve this ? Thanks
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I reproduced the problem when I set the two factors with the same name.
And when I used the different names, it works fine.
So, I guess that you maybe used the same factor name.

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Also, make sure the factor names do not contain spaces or start with a number.

Thanks a lot for looking into it. I had different factor names and no spaces or number.

The first factor is say “AB” with Factor levels CD and EF
The second factor is say “XY” with Factor levels CD and EF

So the factors have different names, while factor levels have same names.
I was able to run limma-voon with the data and so I am not sure what is going on.


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My version is " DESeq2 Determines differentially expressed features from count tables(Galaxy Version". And it can run very well with the settings you described.
I can’t upgrade to the version ( It always showed me already installed, but the icon of DESeq2 was not green in the tool list. So I can’t test the newest version on my galaxy container.
Maybe you can try the version (

This is the legend of the graph. I suggest that you can try AB_CD and AB_EF with the first level, and XY_CD and XY_EF with the second level.

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