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I want to use perpendicular offsets in the built-in FindFit function. Are there any possible ways or do I have to code everything by myself?

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Mathematica does not yet have explicit support for orthogonal regression / total least squares, but one can certainly use the built-in optimization functions to implement this sort of fitting. –  J. M. May 7 '13 at 8:00
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Look here cf.net16.net/odlsf –  PlatoManiac May 7 '13 at 10:15
    
For Mathematica examples of orthogonal fitting, see this and this. –  J. M. May 7 '13 at 13:19

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