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If you got a boost from transferring from San Fran to Seattle, overtime it would even out during merit pay-raises. Companies that are large enough to support development offices in both Seattle and Bay Area, are large enough to have a very formalized process for raises, which take into account your current pay vs the local market rate for that position.

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From what I've heard from friends at big companies, the primary variable in the merit process is your current Salary - it does take the other things into account, but almost never enough to make as much of a difference as your current Salary. That's why people stress that it's so important to negotiate your starting salary higher, and not expect to get paid better once in the company.

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