Flowjo 10 apply compensation matrix3/29/2024 You can compensate in FlowJo either by creating a new matrix from compensation controls run with these new data (recommended) or you can load a matrix exported from a previous experiment. New Files don’t have an acquisition matrix (uncompensated) Therefore, we need to compensate these new data first. However, if you load data into a template that has not yet been compensated, the gates will not automatically apply because the gates in the template were created on compensated parameters and these new data don’t have any compensated parameters yet. When a template is created on compensated parameters, and new data is loaded that was compensated on the machine (includes an acquisition matrix), these data will load right into the template and gates will be applied. Applying new compensation matrices to data loaded into templates can be a bit confusing.
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