Check out FlatSNREstimator script. You need two flats and one bias (or one flat dark instead of a bias). Raw, undebayered frames. This should give an average gain across the color channels.
You may also use SplitCFA script to split all frames into separate channels, and run the script on each channel separately. You will typically see differing signal, noise, and SNR's, but nearly equal gains. See the FlatSNREstimator script documentation for an example, section 3.2.
Regards,
Mike
PS: Double check that the flats are well exposed. The script won't work for extremely underexposed or overexposed/saturated/clipped flats.