I guess u're writing your request in wrong form. Try something like this

FourierDCT[diff]

I downloaded your file and ran it in Mathematica. This is what i have as a result:

Attachments:

I guess the data in file diff.txt is not in a proper format. I'm not that acknowledged in this spehre of math, you know. But Mathematica keeps giving me the same error reply:

FourierDCT::fftl (then it's listing arguments from file) is not a non-empty list or rectangular array of numeric quantities.

If u haven't tried, u can read this article for help Discrete Fourier Transforms

P.S I've tried running an example and it works perfect

Hope I've helped you a little bit. And if u solve your problem, I'll be glad to know the answer :)