variance stablisation normalization (VSN).
While the maths are well beyond the capabilities of this biologists, the way my mathematically inclined friend Patricia explained it is that it uses clever statistics to re-evaluate the apparent ratios. These magical formulas tend to improve ratio suppression and coisolation instances.
More tangible perks: The software is free, appears well supported and commonly updated, and has a colorful and friendly looking user interface.
Still doing iTRAQ? Maybe you should check this out!
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