Please ignore - I found the problem.

Thanks

Hello,
I have a question on 2 factor design.

I have a design with 2 factors, with duplicates. Here is the design:

                strain  time
      strain   time
sample1 mut     a 
sample2 mut     b 
sample3 wt      a
sample4 wt      b
sample5 mut     a
sample6 mut     b
sample7 wt      a
sample8 wt      b
Can this be run using DESeq2 in order to investigate the interaction?
I am getting the following error:

"factor levels were dropped which had no samples"

Is this possible to do, or maybe I have an error in my DESeq script?

This is a message to inform the user that one or more factor variables in the column data (and included in the design) had other levels which were not represented by samples in the column data. This would lead to a problem with building the model matrix, if we didn't internally fix this by dropping those levels.

Before you construct the dds, you can see the levels of your factor variables like so:

levels(coldata$strain)

But the message requires no extra effort from the user, the problem is solved inside the constructor function.