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how to estimate the error of FTIR spectra in transmission, especially on the wavenumber ? please

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For statistical error, simply make the measurement a number of times and analyze the set. Systematic error can be harder to track down. The best thing to do is to use a calibration sample with known, sharp lines to see how well your spectrometer reproduces them, and how stable are your measurements over time. For an FTIR, you could easily use the CO$_2$ and H$_2$O vibrational spectra as a standard reference since those are already present in air. Then look up those spectra on the NIST database to see how close you are over the range of interest. This will give you an idea of you wavenumber error.

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