Hello Sir, Thank you for your reply for the previous question.

https://support.bioconductor.org/p/118839/

I have a small doubt Suppose i need to compare two genotypes at two points for two conditions (mock and infected), let the genotypes be A and B and the time point 4dpi and 2 dpi while conditions mock and infected . I have put the contrast command and got

res2 = results(dds, contrast=list( c("time4dpivs_2dpi","GenotypeA.conditioninfected") )) - mock i have taken as reference Does this mean that the log2fold change i will get will be of genotypeA at 4 dpi vs 2dpi after comparing mock and infected of this genotype at each time point ??

As previously, I recommend that you work with a local statistician to help you analyze your data set, particularly for a complex design like this one.