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I am looking at the specs of a BenQ projector and trying to understand it's output frequency.

On page 74 of the manual, there are specs for vertical, horizontal and "pixel" frequency. What does pixel frequency mean?

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Pixel frequency, also known as dot clock is referring to the bandwidth of the projector's controller chip.

For a resolution a certain data rate is required to display all the data (not pixel frequency, see later) - it can be for example:

A resolution of 800x600 at 60 Hz would require:

800 x 600 x 3 (RGB) x 60 Hz/2 (interlaced frame rate) = 43 200 000 bytes per second

or divided on 1024^2 = 41.2 Mb/s, as data rate with full 8-bit color-depth.

To calculate the projector/monitor's bandwidth you will need accurate timing measurement available, but you can get close by using the vertical frequency and compensate for VBLANK (vertical blanking which is a sync feature) with about 5% and HBLANK with about 30%:

So with 800x600 resolution at 60 hz:

800x1.3 x 600x1.05 x 60 = approx. 39 Mhz

The closer these two results get the better it is as that will tell that the projector/monitor is capable to handle the needed data rate to get full resolution, color depth as so forth.

The bandwidth becomes a factor when showing video in particular.

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