Fri May 20, 2016 12:45 pm by sfauteux
Hi MarcelaAh
One thing you can do is download the matlab tool that Dana Pe'er lab made publicly available on their website. This allows you to make a ViSNE Graph over which you can apply phenograph clustering.
The way I do it is:
1: In FlowJo, I gate the desired subset and export the FCS of this particular gate.
2: Transform your data if necessary in the matlab implementation (arcsinh 5 for Mass).
3: Subsample
4: Select the parameters for your ViSNE and run the algorithm (right click)
5: after Visne ran, you will see appear two more parameters bh-SNE1 and 2.
6: Select bh-SNE1 and 2, right click and run phenograph. This will add another parameter phenograph. And then you're done.
7: If you export from matlab this sumbsampled FCS, you can use it in FlowJo to make overlays. ie: You may at some point want to display that Visne (linear scale usually from -50 to 50 range for both axes) in a Flowjo Layout and apply phenograph populations by overlaying.
S