Compensation in Flow cytometry! - (Dec/29/2007 )

Hi everybody,
Could you please explain about the compensation concept in flow cytometry for me? I had confused with it when I performed FACS analysis. I observed that the cell population seemed to be different whenever I changed the compensation of FL1 (FITC) and FL1 (Cy3). Could you help me to show the importance of this concept in FACS, as well as some hints to modify or adjust this parameter for analyzing?
Thank you so much for your help!
Thanh Thuy

Compensation is a means of using mathematics to "compensate" for the fact that a given fluorophore (e.g. FITC) will give some residual fluorescence in another channel (PE, FL2). On http://www.drmr.com/compensation/ you can find basics on compensation.