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I'm dealing with a PWM generator which drives a load at 12V with pretty high currents (5-10A) The PWM frequency is in the band of 100-200 Hz. Which is the best choice and right configuration of ferrite beads to achieve the best filtering of EMI?

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What makes you think you have problems at this 100-200 Hz frequency? More than likely the frequency of problem may be entirely different. Depending on your application, adding capacitance at the load may help. –  Erik Friesen Jun 17 at 13:00

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Which is the best choice and right configuration of ferrite beads to achieve the best filtering of EMI?

Ferrite beads will prove fairly useless at such a low frequency. They tend to start becoming useful in the area above 10 MHz. I'd consider LC filtering but the precise way depends on your particular circuit. Here's some general info on ferrite beads:

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Thanks. Could you suggest any other option which does not involve the construction of a filter. In example EMI gaskets or a metal enclosure, which effect do these have on low frequencies? –  Francesco Jun 17 at 11:25
    
I'm sorry but the only effective treatment for such low frequencies are passive inductors and capacitors and maybe mu metal enclosures. A conventional metal enclosure will only start having some gradual effect in the kHz and higher range. An emc gasket is fairly useless even in the tens and hundreds ok kHz. –  Andy aka Jun 17 at 11:30

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