After the transfection of my cell culture, I tried to measure the mRNA expression levels of a few genes including that targeted by my siRNA. All of them were decreased in the same pattern including most house keeping genes tested, although cell viability and proliferation was not affected!

Although I could find a stable HKG that was not affected, it is still difficult to attribute the results to changes in the target gene because other genes are changing as well. You also never know which other genes have been affected because you weren't studying them.