Team velocity compatibility between Kanban and Scrum

We are farily new to agile development and just starting to use Greenhopper for a new project. The initial items we are working on are pretty much foundational tasks. If we started to use Kanban as a method for development initially on our project and then switched to use the Agile method within Greenhopper in 3 months, will this mess up our calcuated velocity? Basically trying to see if the velocity between the two are comparable..or if we would have to start over again to determine our velocity. We are planning on using story points based on fibonacci and then use actual hours for the estimate when the work begins.

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Kanban is generally used to work through prioritised tasks, whereas SCRUM is used generally to work though user stories. In this context Velocity between the 2 systems would not be comparable.

You are considering using Kanban to work through some intial user stories it seems. An option to consider instead is to have a Sprint 0 - http://www.infoq.com/news/2008/09/sprint_zero

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