In my opinion thin film deposition for conductivity measurements should be carried out on a non-conducting substrate otherwise there will be a contribution from the substrate conductivity. Although insulating Si wafers are available they are expensive because the low level of impurities. However for surface roughness measurements I recommend Si wafers as they have roughness in the order of 0.2-0.5 nm while glass substrates roughness range from 3-4nm. In conclusion for electrical and UV-Vis measurements glass is more convenient while Si will be preferred for roughness measurements.

Thank you for the answer, please also comment on the heat treatment/annealing processes after film deposition.

Glass slides will make a fairly good substrate for low temperatures (below 500C) but you have to be aware that Glass is usually soda-lime glass which high enough amounts of Ca and Na (1-5%) to contaminate your films for annealing temperatures above 300C. This should be a concern for electrical measurements. The most appropriate substrate for post-deposition anneals will be Si wafers, mechanical quality is enough. To avoid contributions from the substrate conductivity you can try to grow a thermal oxide (900C in O2 for 5 min should grow a 50-100nm thick oxide), and then deposit your film on top of it.

Thank you for the useful and prompt reply. :)