The remainder of the documentation below is NOT meant to teach you about compensation, simply how to use FlowJo to perform that function.įlowJo computes the compensation matrix on control samples much the way you would manually set the compensation. Also, there may be cases where the instrument is not capable of compensating between certain channels (for instance, to correct for the spillover between fluorescein and Cy5PE).įor a description of why compensation is necessary, the underlying concepts behind compensation, and some of the pitfalls of improper compensation, see the " Compensation: A perspective" by Mario Roederer (you need to be connected to a network to view this site). This may be necessary in cases where the compensation was inappropriately set during sample collection (although if the sample was over-compensated, then there is no recourse). FlowJo gives you the ability to compensate your data.
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