Asymco‘s Horace Dediu, an independent analyst with a knack for generating eye-opening charts (see here and here), has done it again.

This time he examines the question of whether Apple’s (AAPL) shares are over-valued.

The stock has certainly had a good run. At more than $290 a share Apple is now, as Dediu puts it, nearly the most valuable company on the planet.

“There is a theory,” he writes, “that ultra-large market caps are reserved for companies that are past their prime.”

But large is not what it used to be.

During past market booms, Dediu points out, market caps reached as high as a trillion dollars. Today, the largest market cap on any U.S. stock exchange is Exxon Mobil (XOM) at a little over $314 billion. Apple is No. 2 at $267 billion.

“The real question of under/over-valuation,” Dediu writes, “rests on whether the company is growing or not. Valuation is simply the net present value of future free cash flows (plus assets). So the most important determinant of current value is growth in cash flows.”

And when he graphs earnings-per-share growth over the past five years against valuation (using price-to-earnings ratio as a proxy for valuation), Dediu finds that compared with the other nine largest market cap companies — including tech growth stocks like Microsoft (MSFT) and China Mobile (CHL) — Apple is the outlier.

The way Dediu sees it, Apple with a trailing P/E ratio of 22 is still a bargain.

For more, see the commentary on Dediu’s website here.

[Follow Philip Elmer-DeWitt on Twitter @philiped]