When performing normalization of real time PCR results, I found two ways of doing it:


In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.
On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.


The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve.
Which is correct? 


Question: why ions and electrons are at different temperatures in plasma?
Answer: There are lots of different types of plasmas.

In a thermal plasma the electrons and ions will have the same temperature.

In a non-thermal plasma the discharge is driven by some external power supply e.g. capacitatively coupled RF, inductively coupled, pulsed DC E field etc. 

In a non-thermal plasma the electrons generally have a higher temperature than the ions because the energy from the RF or E field couples with the electrons more efficiently. The electrons transfer energy to the gas to sustain the plasma. 

Strictly speaking non-thermal plasmas are not at equilibrium and we cannot necessarily define a temperature, but temperature is generally a useful concept to use.

Collision rates are generally lower for electrons than ions, but not always (e.g. very low energy electrons and SF6 has huge collision rate). 

The reason for the temperature difference is due partly to the driving energy being mostly coupled to the electrons and the partly because the energy is not rapidly transfered by collisions to the neutral gas and ions.