Hello,

I'm using DESeq2 to analyze RNA-seq data. The experiment consists of 2 factors - "concentration" with 3 levels and "strain" with 5 levels. I want to test the effect of just one factor (say, "strain") by using the likelihood ratio test. 

I defined a full model and a reduced model. I am now looking for a way to extract the p-values and fold changes of the "strain" factor only. However, I only found a way to compare between 2 levels of the factor, rather than get a single value for the entire factor.

Is that even possible?

Thanks

Nofar