A lot of cheap RGB LED setups use PWM to vary the brightness of each component for RGB mixing to produce the full rainbow of colors.
If the carrier frequency of the PWM is too low, a visible flicker can be seen, especially in your peripheral vision.
The real way to vary the brightness is by varying the voltage to the LEDs, of course, but my understanding is that circuitry to do that well is much more complicated, and requires a lot more than just a 5V pinout on a digital IC.
How is RGB brightness implemented in the Procyon and Kasina?
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