Optoelectronic properties can be affected by the types of glass you are using in thermal deposition process. My suggestion is use only Na/K free glass from Schott or Corning. You have to clean all the glasses in proper process to get superior quality results.
Of course substrates can play a crucial role in determining the fundamental properties of thin films. For systematic study your must try to keep the substrate same all the time. If you want to investigate the effect of the substrate then you must keep other parameters constant.