Click one of the two Compensation icons to open the Compensation Wizard: Figure 1
Load your single-stained controls into FlowJo, and make sure they are all added to FlowJo's Compensation group. The acquisition matrix can be modified by double clicking on any compensation matrix badge next to a sample When fcs3.0 files are loaded into FlowJo, the acquisition matrix is applied automatically using the $SPILL keyword embedded within the file. To do this, you will select gates on positive and negative populations for each of these stain, and tell FlowJo to calculate the compensation matrix based on these stains 
FlowJo computes the compensation matrix on control samples much the way you would manually set the compensation. Therefore, a copy must be created in FlowJo that can be edited Double-clicking the grid opens the matrix editor : FlowJo does not allow direct editing of the acquisition matrix to maintain the integrity of the FCS standard since these compensation values are stored within the file. When you are ready to proceed to a more complete overview of the new compensation work flow, please see this document. One other document you will likely find useful is: Applying/Renaming - the matrix, a small overview. 
The compensation matrix is represented by the grid to the left of the sample name The Matrix editor - used to view/adjust matrix numbers with a preview of the changes. Applying Compensation Matrix Create new, apply old, or compare different matrices.
The compensation matrix is represented by the grid to the left of the sample name.Find more FlowJo tuto. Home FlowJo compensation matrix tutorial Applying Compensation Matrix in FlowJo - YouTubĬreate new, apply old, or compare different matrices.
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