My data deals with a treatment which is known to regulate the expression of some known genes. However, upon analyzing the dataset of this treatment, those genes were not present in the list of differentially expressed genes. As such, I wanted to ask what could be the reason of this?

The support site is for technical help with the packages. This is off-topic here. You could post elsewhere, such as biostars.org or reddit, but if you do then add details on what you do, both experimental design and analysis so far, as by now it lacks any details.