Estimation of CCD/CMOS sensor noise
Instead of capturing with shutter on, I suggest you to capture a picture in low-light and set your exposure time as minimum as possible and the reduce the aperture. Capture a neutral surface(where R,G,B are equal,preferably neutral gray) so when averaging the entire frame you will know noise level change by particular color.Do your calculations on Bayer RAW instead of jpeg because RAW is directly from sensor without any extra processing.


  Do you think lens aperture will play a significant role?


Yes.Lens aperture will play a significant role. If you are reducing the aperture it means the amount of light reaching the sensor is less and it has to be compensated by either increasing exposure time or the gain(Increasing the gain increases the noise).