There are various methods to determine the the number of electrons collected in a given sampling interval (look up - photon transfer curve) but this in itself does not give you what the QE (Quantum Efficiency) is of the device. QE is the measure of how many electrons are generated per photon incidence (always less than 1.0 and in CCD's typically in the 28% range).
You must note that the QE also varies with wavelength as the various dielectric layer thicknesses above the photodiodes emphasize and attenuate at different wavelengths.
The only real answer is that you must calibrate the sensor against a known source or a calibrated detector. There are NIST calibrated detectors available in various supply companies. These devices will have a calibration curve vs. wavelength that you can use to calibrate your device.
Here is a link to calibrated PD's on Thorlabs - search on "Calibrated Detectors". They have detectors that have built in amplifiers and bare detectors even with fibre connections. There are many others that sell them too.