We have FACScalibur in the lab with CellQuest, but for post acquisition analysis, I would like to use FlowJo software. Based on our training, we were taught how to do manual compensation and how to do it properly. However, a lot of articles suggest the use of automatic compensation method. I ought to standardize my protocol for acquisition and analysis but I am quite confused whether I acquire uncompensated data for my samples and compensation controls, or the compensation controls data should be acquired with compensation already. I only started reading and learning about flow cytometry this year and I still have to improve my understanding and techniques with post-acquisition analysis.
Thank you in advance.
Sincerely,
JP