I was having the same exact problem and learned the following trick from those at the Stanford FACS facility. Does anybody know if it is possible to use the logicle transform using FlowJo10? - if so I can not figure out how to do this. I suppose this is a matter of preference, but there may also be some mathematical or statistical reasons for this as well (see Parks et al Cytometry A 2006, Moore et al., Cytomtery A 2012, etc).
I am still using FlowJo9.7.5 instead of FlowJo10 because I prefer the logicle (biexponential) transform over the log or arcsinh transforms. These settings (other than the change to "Event_length" from "Cell_length") are what we have been using in flowjo9.7.5 for cytof1 data using relatively recent cytof1 acquisition software (with updated and corrected dual count calibration, and a lower top of scale that we used with previous versions of the software). I uploaded a screen shot with settings where I tried changing this as suggested. I wonder if the problem is because the "Cell_length" parameter name for the cytof2 software has been changed to "Event_length" and this is why FlowJo 9 with your settings is not forcing it into a linear scale (see upper right side of the screen-shot that Mike posted)? Perhaps you can try changing to this. Once you have successfully created a CyTOF-related workspace, then you can reopen that workspace for new files. So, you really do need to close that initial workspace, switch your preferences, then open a new one. In all the v9.x versions of FlowJo I've used, I've *never* been able to get it to successfully switch Preference types while a Workspace window is open. Select your new set of CyTOF preferences. Select "Save This Set of Preferences", name it, and save.ħ. At the middle bottom, click the dropdown menu. I think it's the Width basis that helps shove the plots off the origin (up, and to the right) so you can more easily draw gates on the negative populations.Ħ. Add Time and Cell_length to the linear box.Ĥ.
Click "Define" to open the right-hand pane in the attached picture. In the lower right, check the CyTOF box, and have log parameter range set to 20000 (perhaps 9000, if you're using a CyTOFv2).ģ. Close the empty Workspace that appears.Ģ. I have attached a screenshot of what I have my settings at (currently using 9.7.5).ġ. However, if you're using a Mac FlowJo 9.x, you'll have to change your Preferences. You'll want to have Time and Event_length (or Cell_length) in Linear scaling. Mac FlowJo X allows you to switch scaling type (linear vs log, etc) and length of axes (1e4, 1e5, etc).
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