I used UBC, GAPDH and Beta actin as housekeeping genes in my proximal colon samples. Bu my each Cq calculation shows difference according to housekeeping gene that I analyzed. For instance the Cq values of one housekeeping genes are higher and the other one's Cqs are lower than the target gene which then affect my calculations. These things made me confused.

Considering the fact that housekeeping genes show difference according to tissue type, treatment etc. So how do you decide which housekeeping gene you are gonna use?

Thank you!