The noise is called EMF bleed over. TO fix it:
1) Double check your ground connection on the head unit. Make sure you are grounded either to the harness (and that it's tight and no part of the wire is exposed).
2) If you have an amp double check that ground also, make sure you are grounding to the chasis where there is no paint. Also, run the RCA wires down one side of the car and the power wires down the other. This is a very common cause for the whine you get because the frequency bleeds from the power wire through to the RCA cables.
Make sure you're not using cheap RCA wires and/or other cables. Sheilding really helps in these cases.
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