Inphase (I) and Quadrature (Q) components of signals

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But the amplitude of values is between -3.25*10^4 and 3.25*10^4.

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Don't think in decimal, think in power-of-2 3.25e4 = 2^15, so you're simply displaying a 16-bit signed integer number.

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I'm using the NCO function in DSP Builder (simulink) to display the values. I connected the 16 bit sine and cosine outputs to simulink Scope to display the values. I think the reason of having these big amplitudes is because these values are displayed as signed integer. To fix the issue,

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Why do you think this is an "issue"? Its merely a scale factor.

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I used Output AlteraBlockset to specify [Number of Bits].[] = 1 for the sign bit and [].[Number of Bits] = 15 for the fraction part of the floating point number. So MSB is the sign bit and the rest of 15 bits is the fraction number.

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What you are trying to do sounds reasonable, however, I don't use Simulink, so I cannot comment on whether this is the correct way to convert to fractional integer.

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However, the output values are all negative and the cycle lenght is not correct, either. Or should I use another tool to check these values?

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It sounds like there is something wrong with your method of conversion to fractional integer. I'd take a look at the MATLAB documentation and try to find an example that works :)

Cheers,

Dave