This post deals with compensation matrix file issues for our Mac version and covers:
- Comp matrix file format
- Loading a comp matrix file
- Comp parameter default naming
If you save a compensation matrix from flowjo and open the file In a text editor (say TextWrangler), you can see that the values are tab separated with end-of-line CR (Mac classic). The Parameter names in the text file have to match the parameter names in your FCS data file. (click image below to enlarge)
Loading a comp matrix file
From the "Platform : Compensate : Load Matrix Form File" menu item in Flowjo v9, pick your matrix file.
(If someone sent you the matrix file and it is greyed out, the file type may not be TEXT. Some servers will change the HFS filetype. No worries. Open the file in TextWrangler and resave, or use the Terminal unix command SetFile. i.e. SetFile -t TEXT filename
If your matrix list gets long, one can remove an unused matrix from the matrix list in V9.
Comp parameter default naming
By default, FlowJo v9 will name compensated parameters by enclosing the original parameter name with < >. If you want to change the default for a matrix, edit the matrix file changing the " < >" to what you like, maybe "Comp_" like in our Java version v7.6.5.
One can also load a Flowjo v9 matrix file into our Java version, v7.6.5, if it is named with the .mtx extension.