Without more context I can't be sure, but I would tend to think that this means: 'Y is different to X'. Does this fit the rest of the context?

@Tresley : I don't think so, here it's really maths we're speaking of, and afaik varier en fonction de is translated by to vary with.

If this were about being different, the correct way to write it would be: 'Y is different from X'. But indeed, the context is mathematics. You could say 'Y depends on X'.

Didn't you notice that I am in the UK? 'Different to' is used in the UK. See here: http://www.worldwidewords.org/qa/qa-dif1.htm

If you are talking mathematics, I believe one would say "Y is a function of X" (I studied applied mathematics 25 years ago, so I hope my memory is still accurate!)

I'm a long time after the fact on this thread, but, being a mathematical expression, shouldn't this be "Y is directly proportional to X" ?

Yes, this is another possibility. "Y is directly proportional to X" is a very particular dependence of Y on X. It is valid only if Y=kX. But most of functions are nor proportional. Example: Y=X*X or Y=sin(X).