How to calibrate a thunderbolt display?

I have calibrated both my macbook pro and thunderbolt display with a Spyder 3 and they look totally different, any ideas?

Well, with the spyder elite 4 software you can choose to calibrate both monitors to match each other. I did this over the weekend.
You have to pay attention to screen brightness. I used the laptop keyboard to adjust the brightness on the laptop monitor when prompted, and used the external keyboard to adjust the brightness on my thunderbolt display when prompted.
I'm not really pleased with the calibration but they are both really similar. You can see large horizontal shadows on the thunderbolt display after the calibration, I suppose it has something to do with the monitor's design. It's really distracting.

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