Hi! I am still learning my RNA-Seq analysis and would greatly appreciate some help here.

Our study is to investigate the pathways associated to interferon-gamma (IFNg)-induced control of infection with bacteriaX. There are four experimental groups (done as 3 biological replicates):

1) Uninfected without IFNg
2) Uninfected with IFNg
3) BacteriaX infected without IFNg
4) BacteriaX infected with IFNg

I aligned the data to the hg19 reference genome using TopHat2 followed by HTSeq Count. My question is on the DESeq2 part: what we are really interested is the transcriptional changes associated to both infection and the presence of IFNg.

Is it possible to normalize condition 3 to condition 1 and condition 4 to condition 2, before performing DESeq2?

Or are there more approporiate ways to analyze the data?

Any suggestions will be greatly appreciated! Many thanks in advance!